Convalescent plasma as adjunctive therapy for hospitalized patients with COVID-19:The Co-CLARITY Trial

Background and Objective@#Convalescent plasma therapy (CPT) may reduce the risk of disease progression among patients with COVID-19. This study was undertaken to evaluate the efficacy and safety of CPT in preventing ICU admission among hospitalized COVID-19 patients.@*Methods@#In this open-label randomized controlled trial, we randomly assigned hospitalized adult patients with COVID-19 in a 1:1 ratio to receive convalescent plasma as an adjunct to standard of care or standard of care alone. The primary endpoint was ICU admission within first 28 days of enrolment. Primary safety endpoints include rapid deterioration of respiratory or clinical status within four hours of convalescent plasma transfusion and cumulative incidence of serious adverse events during the study period including transfusion-related acute lung injury (TRALI), transfusion-associated circulatory overload (TACO), severe allergic reactions, and transfusion-related infections.@*Results@#A total of 22 patients were assigned to receive convalescent plasma as an adjunct to standard of care and 22 to receive standard of care alone. The median time from onset of COVID-19 symptoms to study enrolment was eight days (IQR, 4 to 10). Two patients (9.1%) in the CPT group and one patient (4.5%) in the control group were admitted to the ICU. The primary outcome measure, ICU admission, was not different between the two groups (q-value >0.9). No patient who received convalescent plasma had rapid deterioration of respiratory/clinical status within four hours of transfusion and none developed TRALI, TACO, anaphylaxis, severe allergic reactions, or transfusion-related infections. There was also no significant difference in the secondary outcomes of 28-day mortality (two patients in the CPT group and none in the control group, q-value >0.90), dialysis-free days, vasopressor-free days, and ICU-free days.@*Conclusions@#Among hospitalized COVID-19 patients, no significant differences were observed in the need for ICU admission between patients given CPT as adjunct to standard of care and those who received standard of care alone. Interpretation is limited by early termination of the trial which may have been underpowered to detect a clinically important difference.

Exposure of reproductive-aged pregnant and nonpregnant women to common environmental pollutants and endocrine-disrupting chemicals A cross-sectional survey at the University of the Philippines-Philippine General Hospital / Philippine Journal of Obstetrics and Gynecology

Context@#Exposure to environmental pollutants (EP) and Endocrine-disrupting chemicals (EDCs) is associated with several general negative health effects which compromise women's reproductive health, maternal, and neonatal outcomes. Unfortunately, many nonpregnant and pregnant women are unaware of their active exposure to these potentially slow-acting toxic substances, EPs, and EDCs. At any stage of life, and in the long-term minute exposures, there is no established safe level of exposure to these substances. Due to the potentially harmful effects on women in general, and to the pregnant and her unborn child in particular, it is important to establish the prevalence of their exposure. @*Aims@#The aim of this study was to determine the magnitude (prevalence) of exposure among nonpregnant and pregnant women aged 18–49 years to common EPs/EDCs such as bisphenol A, pesticides, phthalates, and perfluorinated compounds among others.@*Settings and Design @#This study was conducted at the Philippine General Hospital, University of the Philippines Manila.@*Subjects and Methods @#The study participants were nonpregnant and pregnant women, with low-risk singleton pregnancy, and had a prenatal checkup and eventual delivery at the Philippine General Hospital. After consent, women were asked to answer a survey focused on their sociodemographics and frequency of exposure to EP- and EDC-containing items.@*Satatistical Analysis Used@#Descriptive statistics were used to summarize the demographic and clinical characteristics of the patients. Null hypotheses were rejected at 0.05 α-level of significance. The computer software STATA 13.1 was used for data analysis.@*Results@#One hundred and fifty-nine survey responses by women were analyzed. Possible EDC-containing household items (carpets, linoleum, upholstered, and stain-resistant furniture) are more prevalent in the homes of pregnant women compared to nonpregnant women. Pregnant women are also exposed to wallpapers compared to nonpregnant individuals. Nonpregnant women were 1.5 times more exposed to lotions. Unexposure to hand sanitizers is 1.3 times higher among pregnant individuals.@*Conclusions@#There are differences in the prevalence of exposure to household EDC-containing items between pregnant and nonpregnant women, with pregnant women having a higher prevalence of exposure.

Epidemiología de pacientes con hepatocarcinoma en un hospital Universitario / Epidemiology of patients with hepatocellular carcinoma in a University hospital

Resumen El carcinoma hepatocelular (HCC) es el tumor primario más frecuente del hígado, con 905 677 casos diagnosticados en 2020, en todo el mundo, y 830 180 muertes. Es responsable de la novena causa de muerte por cáncer en los hombres y la décima en mujeres en Argentina. A diferencia de otros tumo res de alta prevalencia, la evidencia científica acerca del HCC se limita principalmente a pequeñas cohortes y estudios retrospectivos. El objetivo de este estudio fue describir epidemiológicamente a aquellos pacientes con diagnóstico de HCC en el Hospital Italiano de Buenos Aires en un periodo de 12 años. La supervivencia global para nuestra cohorte fue de 58, 46 y 36% a 1, 3 y 5 años respectivamente. El promedio de supervivencia en pacientes con tratamiento paliativo fue de 5 meses, 23 para aquellos que recibieron tratamientos no curativos y 75 meses para los que recibieron tratamientos curativos. El porcentaje de pacientes libres de enfermedad a 1, 3 y 5 años fue de 89%, 76% y 61% respectivamente. Se realizó un estudio minucioso de la etiología, factores de riesgo, incidencia, mortalidad y tratamientos realizados. Su importancia yace en su tamaño muestral, calidad y cantidad de información disponible.

Abstract Hepatocellular carcinoma is the most common primary liver tumor, with 905 677 diagnosed cases and 830 180 deaths, in 2020 worldwide. In Argentina, it accounts for the 9th cause of death for cancer in men and the 10th in women. Unlike other highly-prevalent tumors, scientific evidence for most therapeutic options is limited mainly to small cohorts and retrospective studies. The aim of this study is to characterize and describe epidemiologically patients with diagnosis of hepatocellular carcinoma in the Italian Hospital of Buenos Aires during a 12-year period. Overall survival for our cohort was 58%, 46%, and 36% at 1, 3 and 5 years respectively. Average survival for patients receiving palliative treatment was 5 months, while for those who received either non-curative or curative treatment was 23 and 75 months respectively. Recurrence-free survival for those patients who under went a curative treatment was 89%, 76% y 61% at 1, 3 and 5 years. A thorough analysis of etiology, risk factors, incidence, mortality and treatment was made. The study's importance lies in its large sample size, quantity and quality of data, and will most certainly stimulate the development of local studies in hepatocellular carcinoma.

Diretriz Latino-americana sobre o Diagnóstico e Tratamento da Alergia Ocular ­ Em nome da Sociedade Latinoamericana de Alergia, Asma e Imunologia (SLAAI) / Latin American Guideline on the Diagnosis and Treatment of Ocular Allergy ­ On behalf of the Latin American Society of Allergy, Asthma and Immunology (SLAAI)

A alergia ocular, também conhecida como conjuntivite alérgica (CA), é uma reação de hipersensibilidade mediada por imunoglobulina E (IgE) do olho desencadeada por aeroalérgenos, principalmente ácaros da poeira doméstica e pólen de gramíneas. Os sintomas geralmente consistem em prurido ocular ou periocular, lacrimejamento e olhos vermelhos que podem estar presentes durante todo o ano ou sazonalmente. A alergia ocular tem frequência elevada, é subdiagnosticada e pode ser debilitante para o paciente. É potencialmente danosa para a visão, nos casos em que ocasiona cicatrização corneana grave, e na maioria dos pacientes associa-se a outros quadros alérgicos, principalmente rinite, asma e dermatite atópica. É classificada em conjuntivite alérgica perene, conjuntivite alérgica sazonal, ceratoconjuntivite atópica e ceratoconjuntivite vernal. O diagnóstico procura evidenciar o agente etiológico e a confirmação se dá pela realização do teste de provocação conjuntival. O tratamento baseia-se em evitar o contato com os desencadeantes, lubrificação, anti-histamínicos tópicos, estabilizadores de mastócitos, imunossupressores e imunoterapia específica com o objetivo de obter o controle e prevenir as complicações da doença.

Ocular allergy, also known as allergic conjunctivitis, is an immunoglobulin E-mediated hypersensitivity reaction of the eye triggered by airborne allergens, primarily house dust mites and grass pollen. Symptoms usually consist of ocular or periocular itching, watery eyes, and red eyes that may be present year-round or seasonally. Ocular allergy has a high frequency, is underdiagnosed, and can be debilitating for the patient. It is potentially harmful to vision in cases of severe corneal scarring, and in most patients, it is associated with other allergic conditions, especially rhinitis, asthma, and atopic dermatitis. It is classified as perennial allergic conjunctivitis, seasonal allergic conjunctivitis, atopic keratoconjunctivitis, and vernal keratoconjunctivitis. Diagnosis seeks to identify the etiologic agent, and confirmation is given by conjunctival provocation testing. Treatment is based on avoiding contact with triggers, lubrication, topical antihistamines, mast cell stabilizers, immunosuppressants, and specific immunotherapy with the aim of achieving control and preventing disease complications.

Perceptions on susceptibility to exposure to the COVID-19 virus: A qualitative study on pregnant and non-pregnant adult women, their partners, and healthcare workers in Metro Manila

Introduction@#The World Health Organization (WHO) reported that special populations are more susceptible to the COVID-19 virus. There is little information on whether COVID-19 affects women of reproductive age and their fertility, pregnancy status, and offspring give: We aimed to assess the knowledge, practices, and perceptions (KPP) on the risk and susceptibility to COVID-19 of women of reproductive age. @*Methods@#We conducted a qualitative exploratory descriptive study using the triangulation method. The study consisted of in-depth interviews (IDIs) with women of reproductive age and their spouses, focus group discussions (FGDs), and key informant interviews (KIIs) with health care professionals (HCP) in University of the Philippines-Philippine General Hospital. We assessed KPP using structured, open-ended interview guides. Interview responses were recorded and transcribed verbatim, and thematic analysis was performed using NVivo 12. @*Results@#Eighty participants, 20 women of reproductive age, 20 spouses, 20 non-pregnant women, and 20 HCPs in UP-PGH were included in the study. All participants were knowledgeable about COVID-19. Pregnant women would consult their physicians when they felt symptoms related to COVID-19. Spouses of pregnant women and non-pregnant women observed health measures to prevent the spread of the virus. Both pregnant and non-pregnant patients with COVID-19 felt shamed and stigmatized while the husbands worried that the exposure to the infection will pose a burden to their families. HCWs provided services through teleconsultation and found it challenging to refer patients to other facilities. @*Conclusion@#The study provided insights on KPP of women with reproductive-age to COVID-19 and views of HCWs in providing care to these patients during the pandemic. The effects of COVID-19 are still detrimental and highly evident from the micro to the macro level.

Endometriosis pleural. A propósito de un caso / Pleural Endometriosis. A Case Report

La endometriosis extrauterina es una enfermedad poco frecuente que afecta a mujeres en edad reproductiva. La cavidad pleural es una de las localizaciones más frecuentes en este tipo de patología y es en ella donde se puede encontrar con mayor frecuencia neumotórax de repetición seguido por hemotórax. La afectación parenquimatosa, al igual que el hemotórax, es poco frecuente1. Presentamos el caso de una mujer en edad fértil con hemotórax debido a endometriosis pleural.

Extrauterine endometriosis is a rare disease that affects women of childbearing age. The pleural cavity is one of the most common locations of this type of disease and the place where recurrent pneumothorax followed by haemothorax most frequently occur. Paren chymal involvement and haemothorax aren't very frequent1. We present the case of a woman of childbearing age with haemothorax due to pleural endometriosis.

Soporte circulatorio con ECMO venoarterial en paciente con cardiomiopatía de Takotsubo biventricular / Circulatory support with venoarterial ECMO in a patient with biventricular Takotsubo cardiomyopathy

Resumen La cardiomiopatía de Takotsubo es una entidad caracterizada por disfunción ventricular aguda y transitoria, la cual está generalmente relacionada a un evento desencadenante (estrés emocional o físico) y que, por lo general, se presenta con disfunción sistólica regional del ventrículo izquierdo, aunque hasta en un 30% puede ser biventricular. Según su severidad, en algunos casos puede condicionar choque cardiogénico refractario a manejo con inotrópicos y vasopresores, por lo que para estos casos deben considerarse los dispositivos de asistencia circulatoria. Presentamos el caso de una paciente joven a quien se realizó cambio valvular pulmonar con prótesis biológica, la cual siete semanas posteriores a la cirugía acudió al servicio de urgencias con derrame pericárdico y fisiología de tamponade secundario a síndrome pospericardiotomía. Por tal motivo se le practicó ventana pericárdica, sin embargo durante el transquirúrgico presentó cardiomiopatía de Takotsubo biventricular que le condicionó choque cardiogénico con insuficiencia mitral y tricúspidea severas y refractariedad a tratamiento médico, así como a balón intraaórtico de contrapulsación (BIAC), por lo cual requirió soporte circulatorio con ECMO venoarterial durante 5 días.

Abstract Takotsubo cardiomyopathy is an entity characterized by acute and transient ventricular dysfunction, which is usually related to a triggering event (emotional or physical stress), and usually presents with regional systolic dysfunction of the left ventricle, however up to 30% may be biventricular. Depending on its severity in some cases the disease can condition refractory cardiogenic shock to management with inotropics and vasopressors, so for these cases circulatory assistance devices should be considered. We present the case of a young patient who had pulmonary valve change with biological prosthesis, which seven weeks after surgery went to the emergency department with pericardial effusion and tamponade physiology secondary to postpericardiotomy syndrome. For this reason pericardial window was practiced, however during the procedure she presented biventricular Takotsubo cardiomyopathy which conditioned cardiogenic shock with severe mitral and tricuspid regurgitation, and refractivity to medical treatment as well as intraaortic balloon pump, requiring circulatory support with venoarterial ECMO for 5 days.

COVID-19 recommender system based on an annotated multilingual corpus

Tracking the most recent advances in Coronavirus disease 2019 (COVID-19)‒related research is essential, given the disease's novelty and its impact on society. However, with the publication pace speeding up, researchers and clinicians require automatic approaches to keep up with the incoming information regarding this disease. A solution to this problem requires the development of text mining pipelines; the efficiency of which strongly depends on the availability of curated corpora. However, there is a lack of COVID-19‒related corpora, even more, if considering other languages besides English. This project's main contribution was the annotation of a multilingual parallel corpus and the generation of a recommendation dataset (EN-PT and EN-ES) regarding relevant entities, their relations, and recommendation, providing this resource to the community to improve the text mining research on COVID-19‒related literature. This work was developed during the 7th Biomedical Linked Annotation Hackathon (BLAH7).

Universal definition of perioperative bleeding in cardiac surgery adults and association with mortality in a Mexican Cardiovascular Critical Care Unit / Definición universal de sangrado perioperatorio en cirugía cardiaca adultos y asociación con mortalidad en una Unidad de Terapia Intensiva Cardiovascular de México

Abstract Background: Bleeding as a complication is associated with poorer results in cardiac surgery. There is increasing evidence that the use of blood products is an independent factor of increased morbidity, mortality, and hospital costs. Dyke et al. established the universal definition of perioperative bleeding (UDPB). This classification is more precise defining mortality in relation to the degree of bleeding. Methods: A descriptive and analytical retrospective study of a database of patients underwent cardiac surgery from January 1, 2016, to December 31, 2017, was performed. The primary objective of the study was to look at mortality associated with the degree of bleeding using the UDPB. Results: A total of 918 patients who went to cardiac surgery were obtained. Most of the population was classified as insignificant bleeding class (n = 666, 72.9%), and for massive bleeding the lowest proportion (n = 25, 2.7%). For the primary outcome of 30-day mortality, a significant difference was found between the groups, observing that it increased to a higher degree of bleeding. This was corroborated by multivariate logistic regression analysis that was adjusted to EuroScore II and cardiopulmonary bypass (CPB) duration, finding an independent association of the bleeding class with 30-day mortality (OR, 95%, 5.82 [2.22-15.26], p = 0.0001). Conclusions: We found that the higher the degree in UDPB was associated with higher mortality independently to EuroScore II and CPB duration for adult patients undergoing cardiac surgery.

Resumen Antecedentes: El sangrado como complicación está asociado a peores resultados en cirugía cardiaca. Existe una evidencia cada vez mayor que la transfusión de productos sanguíneos por si solo es un factor independiente de incremento en la morbilidad, mortalidad, y costos hospitalarios. Dyke y colaboradores establecieron la definición universal de sangrado perioperatorio. Esta clasificación es más precisa en definir mortalidad en relación con el grado de sangrado. Material y métodos: Se realizo un estudio descriptivo y analítico de tipo retrospectivo de una base de datos de pacientes que fueron a cirugía cardiaca del 1 enero del 2016 al 31 de diciembre del 2017. El objetivo primario del estudio fue observar la mortalidad asociada con el grado de sangrado utilizando la definición universal de sangrado perioperatorio. Resultados: Se obtuvieron un total de 918 pacientes que fueron a cirugía cardiaca. La mayor parte de la población fue clasificada como clase de sangrado insignificante (n = 666, 72.9%), y para sangrado masivo la menor proporción (n = 25, 2.7%). En el desenlace primario de mortalidad a 30 días se encontró una diferencia significativa entre los grupos, observando que aumentada a mayor clase de sangrado. Esto fue corroborado mediante un análisis multivariado regresión logística que fue ajustado a con EuroScore II y el tiempo de bomba de circulación extracorpórea, encontrando una asociación independiente de la clase de sangrado con mortalidad a 30 días (OR, 95%, 5.82 [2.22-15.26], p = 0.0001). Conclusiones: Encontramos que cuanto mayor era el grado en la UDPB se asociaba con una mayor mortalidad independientemente de EuroScore II y la duración del bypass cardiopulmonar para pacientes adultos sometidos a cirugía cardíaca.

Cardiotoxicity and cancer: prudential judgment in medical practice / Cardiotoxicidad y cáncer: el juicio prudencial en la práctica médica

ABSTRACT The objective of this paper is to propose a conceptual tool for consideration by medical professionals and cardiologists, based on the concept of prudential judgment or Aristotelian phronesis to confront the problems of cardiotoxicity resulting from cancer treatments. We start by analyzing the case of a young female patient who received two types of therapies: the first with anthracyclines (adriamycin), which produces type I damage, as stated in the consensus of 2014; and the second treatment, one month later, with trastuzumab, an agent that produces type II damage not dependent on dose. In this case, the patient manifested acute cardiac insufficiency, with a decrease of LVEF to 28% on the echocardiogram and to 27% on magnetic resonance imaging. Reports have indicated that treatment with beta blockers and the suspension or decrease of the dose limits damage, but during preclinical stages. Awareness and early attention to subclinical damage have thus become extremely relevant to substantiate treatments based not only on clinical evidence but also on the ability of medical professionals to rely on prudential judgment--which moves away from the medical practices that are developed on a daily basis in order to influence and reduce the cases of irreversible heart failure known as cardiotoxicity.(AU)

RESUMEN Este trabajo tiene como objetivo proponer el juicio prudencial o phrónesis aristotélica como herramienta conceptual para la deliberación de los profesionales de la medicina y cardiólogos para afrontar la problemática que implica la cardiotoxicidad como resultado de los tratamientos contra el cáncer. Partimos desde el análisis de caso de una paciente joven que recibió dos tipos de terapias: la primera con antraciclinas (adriamicina) que produce daño por el mecanismo tipo I, propuesto en el consenso del 2014, y un mes después con trastuzumab, agente que produce daño tipo II no dependiente de dosis. En este caso la paciente presentó insuficiencia cardiaca aguda, con disminución de la FEVI a 28% por ecocardiograma y de 27% por resonancia magnética cardiaca. Se ha reportado que el tratamiento con betabloqueadores y la suspensión o disminución de la dosis limita el daño cuando se encuentra en etapas preclínicas. Por ello el pensamiento y el abordaje temprano en búsqueda de daño subclínico ha tomado extrema relevancia para fundamentar los tratamientos no solo desde la evidencia clínica, sino también en el juicio prudencial que dejan las prácticas médicas desarrolladas día a día para impactar y reducir estos casos de falla cardiaca irreversible conocidos como cardiotoxicidad.(AU)

Feasibility in the echocardiographic estimation of parameters of the right ventricle in prone position / Factibilidad en la estimación ecocardiográfica de parámetros del ventrículo derecho en posición prono

Abstract Background: Echocardiographic cardiac parameters in the prone position are usually obtained with an esophageal probe. The feasibility of obtaining them by means of a transthoracic approach is unknown. Objective: Estimating the feasibility to obtain parameters of the right ventricle by transthoracic echocardiography in prone position on the subject. Methods: Pilot design of consecutive case series without cardiopulmonary disease. Demographic, vital signs and echocardiographic variables were defined in the ventral initial, prone and ventral final decubitus positions. The data are shown with averages and standard deviations, and frequencies and percentages according to the variable. The differences between the positions were calculated with ANOVA of repeated samples and adjustment of Bonferroni test. Intra-subject variability was obtained by the Bland-Altman procedure and its 95% confidence interval. Results: We studied 50 subjects, 44 (88%) males, age 30 ± 6 years and body mass index 25.65 ± 2.71 kg/m2. Tricuspid annular plane systolic excursion (TAPSE) and S'-wave were measured 100% of the time. The vital signs and echocardiographic variables according to the position had differences in: heart rate (74 ± 9 vs. 77 ± 9 vs. 75 ± 8 beats/min), partial oxygen saturation (94.40 ± 1.70 vs. 96.64 ± 1.79 vs. 95.32 ± 1.36%) and mean systemic blood pressure (65.33 ± 5.38 vs. 67.69 ± 6.31 vs. 65.29 ± 5.62 mmHg); TAPSE (19.74 ± 3.24 vs. 21.60 ± 2.97 vs. 19.44 ± 2.84 mm), mean difference (bias) 0 (2, -2.0) and S'-wave (13.52 ± 1.87 vs. 15.02 ± 2.09 vs. 13.46 ± 1.55 cm/s), mean difference (bias) -0.46 (1.21, -2.14) respectively. Conclusions: Obtaining right ventricle parameters by transthoracic ecocardiopraphy is feasible in the prone position.

Resumen Introducción: Los parámetros cardiacos ecocardiográficos en posición de decúbito prono usualmente se obtienen con sonda esofágica. Se desconoce la factibilidad de obtenerlos mediante aproximación transtorácica. Objetivo: Estimar la factibilidad para obtener parámetros del ventrículo derecho mediante ecocardiografía transtorácica en el sujeto en posición de decúbito prono. Métodos: Diseño piloto de serie de casos consecutivos sin enfermedad cardiopulmonar. Se acotaron variables demográficas, signos vitales y ecocardiográficas en posición decúbito ventral inicial, prono y ventral final. Los datos se muestran con promedios y desviaciones estándar, y frecuencias y porcentajes de acuerdo con la variable. La diferencia entre las posiciones se calculó con ANOVA de muestras repetidas y ajuste de Bonferroni. Se obtuvo la variabilidad intrasujetos mediante el procedimiento de Bland-Altman y su intervalo de confianza al 95%. Resultados: Se estudiaron 50 sujetos, 44 (88%) masculinos, edad 30 ± 6 años e índice de masa corporal 25.65 ± 2.71 kg/m2. El TAPSE (excursión sistólica del plano del anillo tricuspídeo) y la onda S' se midieron en el 100% de las veces. Los signos vitales y variables ecocardiográficas de acuerdo con la posición tuvieron diferencias en: frecuencia cardiaca (74 ± 9 vs. 77 ± 9 vs. 75 ± 8 lpm), saturación parcial de oxígeno (94.40 ± 1.70 vs. 96.64 ± 1.79 vs. 95.32 ± 1.36%) y la presión arterial sistémica media (65.33 ± 5.38 vs. 67.69 ± 6.31 vs. 65.29 ± 5.62 mmHg); TAPSE (19.74 ± 3.24 vs. 21.60 ± 2.97 vs. 19.44 vs. 2.84 mm), diferencia media (sesgo) 0 (2, -2.0) y onda S' (13.52 ± 1.87 vs. 15.02 ± 2.09 vs. 13.46 ± 1.55 cm/s), diferencia media (sesgo) -0.46 (1.21, -2.14) respectivamente. Conclusión: En posición de decúbito prono es factible obtener parámetros del ventrículo derecho por ecocardiografía transtorácica.

Preliminary identification of Human Leukocyte Antigen (HLA) CLASS II DRB1 Allelic variants in selected Filipino cancer patient samples

Objective@#The Human Leukocyte Antigen (HLA) Class II is the major histocompatibility complex surface glycoproteins of humans responsible for presenting exogenous antigenic peptides which help direct specificity of immune response. In immune-cell therapy, the HLA allelic variants are of particular importance as they determine the successful activation of target cells that results to a desired therapeutic response. However, HLA Class II exhibits high polymorphism and has variable distribution in population, constituting these so-called allelic variants. Specifically, the HLA Class II DRB1 is considered the predominant locus among Filipinos. This research aimed to identify the presence of HLA Class II DRB1 allelic variants in the stem cell samples of ten (10) Filipino cancer patients by reverse transcription polymerase chain reaction (RT-PCR) amplification. @*Method@#This study employed a PCR-based HLA Class II typing to identify the HLA Class II DRB1 allelic variant in Filipino cancer patients. Design of forward and reverse primers for HLA Class II DRB1, optimization of PCR conditions for amplifying HLA Class II DRB1, and identification of HLA Class II DRB1 allelic variants from samples by sequencing and database comparison were conducted. @*Results@#PCR optimization showed that optimum annealing temperature for HLA DRB1 was 58.8°C with 1 mM MgCl2. PCR amplification of HLA DRB1 from ten anonymized cancer patient samples and DNA sequencing revealed that Patients 1, 2, 5, 8, 9, and 10 harbor HLA DRB1 allelic variants, particularly, the HLA DRB1*04:06:01, HLA DRB1*12:01:01, HLA DRB1*0813, HLA DRB1*04:05:01, HLA DRB1*09:01:02, and HLA DRB1*16:02:01, allelic variants, respectively.@*Conclusion@#Using the designed primers and optimized RT-PCR protocol, HLA information derived from six out of ten patient samples can be used for further applications in developing personalized or generic antigenic peptides such as dendritic cell cancer vaccine.

In silico prediction of SARS-CoV-2 epitopes for vaccine development

@#The ongoing coronavirus disease (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is causing major damages in health and economies worldwide. The development of safe and effective vaccines for COVID-19 is of utmost importance yet none have been licensed to date. One of the strategies for vaccine development utilizes dendritic cells which express class I and class II human leukocyte antigen (HLA) molecules. These HLA molecules present the antigenic peptides to T cells which mediate the immune response. Thus, the study aimed to identify SARS-CoV-2 peptides with potential binding to HLA class I and class II molecules using different bioinformatics tools. SYFPEITHI and IEDB were used to predict epitopes for the most common HLA class I and II alleles among Filipinos. The top predicted epitopes were subjected to de novo and template-based molecular docking. Then, binding energies of the generated peptide-HLA complexes to putative T cell receptors were predicted using a homology modeling approach. Several predicted epitopes showed promising MHC and TCR binding, although results varied considerably between the prediction methods used. In particular, the results of de novo and template-based docking methods did not coincide, the latter of which generated complexes that more closely resemble typical peptide-HLA complexes. The results of this study will be validated by the next stage of the vaccine development project which is the in vitro assessment of the T cell responses elicited by dendritic cells pulsed with the candidate peptides.

Improving accessibility and distinction between negative results in biomedical relation extraction

Accessible negative results are relevant for researchers and clinicians not only to limit their search space but also to prevent the costly re-exploration of research hypotheses. However, most biomedical relation extraction datasets do not seek to distinguish between a false and a negative relation among two biomedical entities. Furthermore, datasets created using distant supervision techniques also have some false negative relations that constitute undocumented/unknown relations (missing from a knowledge base). We propose to improve the distinction between these concepts, by revising a subset of the relations marked as false on the phenotype-gene relations corpus and give the first steps to automatically distinguish between the false (F), negative (N), and unknown (U) results. Our work resulted in a sample of 127 manually annotated FNU relations and a weighted-F1 of 0.5609 for their automatic distinction. This work was developed during the 6th Biomedical Linked Annotation Hackathon (BLAH6).

Improving accessibility and distinction between negative results in biomedical relation extraction

Accessible negative results are relevant for researchers and clinicians not only to limit their search space but also to prevent the costly re-exploration of research hypotheses. However, most biomedical relation extraction datasets do not seek to distinguish between a false and a negative relation among two biomedical entities. Furthermore, datasets created using distant supervision techniques also have some false negative relations that constitute undocumented/unknown relations (missing from a knowledge base). We propose to improve the distinction between these concepts, by revising a subset of the relations marked as false on the phenotype-gene relations corpus and give the first steps to automatically distinguish between the false (F), negative (N), and unknown (U) results. Our work resulted in a sample of 127 manually annotated FNU relations and a weighted-F1 of 0.5609 for their automatic distinction. This work was developed during the 6th Biomedical Linked Annotation Hackathon (BLAH6).