PEO: Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida.

The Plant Expression Omnibus (PEO) is a web application that provides biologists with access to gene expression insights across over 100 plant species, ~60 000 manually annotated RNA-seq samples, and more than 4 million genes. The tool allows users to explore the expression patterns of genes across different organs, identify organ-specific genes, and discover top co-expressed genes for any gene of interest. PEO also provides functional annotations for each gene, allowing for the identification of genetic modules and pathways. PEO is designed to facilitate comparative kingdom-wide gene expression analysis and provide a valuable resource for plant biology research. We provide two case studies to demonstrate the utility of PEO in identifying candidate genes in pollen coat biosynthesis in Arabidopsis and investigating the biosynthetic pathway components of capsaicin in Capsicum annuum. The database is freely available at https://expression.plant.tools/.

METER (Mental health emergency response) program: Findings of psychological impact status and factors associated with depression, anxiety and stress among healthcare workers in public hospital in Malaysia during the COVID-19 pandemic.

INTRODUCTION: The COVID-19 pandemic has become the greatest challenge of the new millennium. Most healthcare workers (HCWs) experienced unprecedented levels of workload since the pandemic. This study aims to identify the prevalence and factors of depression, anxiety and stress among HCWs in Malaysian healthcare facilities in the midst of the pandemic due to the SARs-CoV-2. METHODS: An emergency response programme on mental health was conducted from June to September 2020. A standardized data collection form was distributed among the HCWs in the government hospital in Klang Valley. The form contained basic demographic information and the self-reported Malay version of the Depression, Anxiety and Stress scale (BM DASS-21). RESULTS: Of the1,300 staff who attended the Mental Health and Psychosocial Support in Covid-19 (MHPSS COVID-19) programme, 996 staff (21.6% male, 78.4% female) completed the online survey (response rate: 76.6%). Result showed that staff aged above 40 years old were almost two times more likely to have anxiety (AOR = 1.632; 95% CI = 1.141-2.334, p:0.007) and depression (AOR = 1.637; 95% CI = 1.1.06-2.423, p:0.014) as compared to staff who were less than 40 years old. Those who had direct involvement with COVID-19 patients were likely to suffer stress (AOR = 0.596; 95% CI = 0.418-0.849, p:0.004), anxiety (AOR = 0.706; 95% Ci = 0.503-0.990, p:0.044) and depression (AOR = 0.630; 95% Ci = 0.427-0.928, p:0.019). HCWs with stress (AOR = 0.638; 95% CI of 0.476-0.856, p = 0.003), anxiety (AOR = 0.720; 95% CI 0.542-0.958, p = 0.024) and depression (AOR = 0.657; 95% CI 0.480-0.901, p = 0.009) showed less confidence to treat critically ill patients and need psychological help during outbreak. CONCLUSION: This study showed the importance of psychosocial support to reduce psychological distress among HCWs when working or coping during the COVID-19 pandemic or outbreak.

The Cross-Sectional Relations of COVID-19 Fear and Stress to Psychological Distress among Frontline Healthcare Workers in Selangor, Malaysia.

Previous pandemics have demonstrated short and long-term impacts on healthcare workers' mental health, causing knock-on effects on patient care and professional functioning. Indeed, the present COVID-19 pandemic has created unprecedented disruption in social interactions and working conditions. Malaysia has been under the Recovery Movement Control Order since June 2020; however, with the upsurge of cases, healthcare workers face pressure not only from working in resource-deprived settings but also from the increasing patient load. The primary objective of the present study was to examine the cross-sectional relationship of COVID-19 fear and stress to psychological distress (operationalized as anxiety and depression) in healthcare workers. The present sample included 286 frontline healthcare workers from three hospitals in Selangor, Malaysia. Self-administered questionnaires containing sociodemographic and occupational items, the Malay versions of the Coronavirus Stress Measure scale, the Fear of Coronavirus-19 scale, the Generalized Anxiety Disorder-7, and the Patient Health Questionnaire-9 were distributed via online platforms. Hierarchical multiple regression findings suggest that age, shift work, and COVID-19 stress consistently predicted anxiety and depression among frontline healthcare workers after adjusting for sociodemographic and occupational variables. The present findings suggest that frontline healthcare workers are not only inoculated against COVID-19 itself but also against the psychological sequelae of the pandemic.

LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life.

MOTIVATION: There are now more than two million RNA sequencing experiments for plants, animals, bacteria and fungi publicly available, allowing us to study gene expression within and across species and kingdoms. However, the tools allowing the download, quality control and annotation of this data for more than one species at a time are currently missing. RESULTS: To remedy this, we present the Large-Scale Transcriptomic Analysis Pipeline in Kingdom of Life (LSTrAP-Kingdom) pipeline, which we used to process 134 521 RNA-seq samples, achieving ∼12 000 processed samples per day. Our pipeline generated quality-controlled, annotated gene expression matrices that rival the manually curated gene expression data in identifying functionally related genes. AVAILABILITY AND IMPLEMENTATION: LSTrAP-Kingdom is available from: https://github.com/wirriamm/plants-pipeline and is fully implemented in Python and Bash. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

LSTrAP-Crowd: prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data.

BACKGROUND: Bacterial resistance to antibiotics is a growing health problem that is projected to cause more deaths than cancer by 2050. Consequently, novel antibiotics are urgently needed. Since more than half of the available antibiotics target the structurally conserved bacterial ribosomes, factors involved in protein synthesis are thus prime targets for the development of novel antibiotics. However, experimental identification of these potential antibiotic target proteins can be labor-intensive and challenging, as these proteins are likely to be poorly characterized and specific to few bacteria. Here, we use a bioinformatics approach to identify novel components of protein synthesis. RESULTS: In order to identify these novel proteins, we established a Large-Scale Transcriptomic Analysis Pipeline in Crowd (LSTrAP-Crowd), where 285 individuals processed 26 terabytes of RNA-sequencing data of the 17 most notorious bacterial pathogens. In total, the crowd processed 26,269 RNA-seq experiments and used the data to construct gene co-expression networks, which were used to identify more than a hundred uncharacterized genes that were transcriptionally associated with protein synthesis. We provide the identity of these genes together with the processed gene expression data. CONCLUSIONS: We identified genes related to protein synthesis in common bacterial pathogens and thus provide a resource of potential antibiotic development targets for experimental validation. The data can be used to explore additional vulnerabilities of bacteria, while our approach demonstrates how the processing of gene expression data can be easily crowd-sourced.

Prolonged interpregnancy interval: how does it impact the length of second stage of labor?

Objectives Short interpregnancy intervals (IPI) have been linked to multiple adverse maternal and neonatal outcomes, but less is known about prolonged IPI, including its relationship with labor progression. The objective of the study was to investigate whether prolonged IPIs are associated with longer second stages of labor. Methods A perinatal database from Kaiser Permanente Hawaii was used to identify 442 women with a prolonged IPI ≥60 months. Four hundred forty two nulliparous and 442 multiparous women with an IPI 18-59 months were selected as comparison groups. The primary outcome was second stage of labor duration. Perinatal outcomes were compared between these groups. Results The median (IQR) second stage of labor duration was 76 (38-141) min in nulliparous women, 15 (9-28) min in multiparous women, and 18 (10-38) min in women with a prolonged IPI (p<0.0001). Pairwise comparisons revealed significantly different second stage duration in the nulliparous group compared to both the multiparous and prolonged IPI groups, but no difference between the multiparous and prolonged IPI groups. There was a significant association with the length of the IPI; median duration 30 (12-61) min for IPI ≥120 months vs. 15 (9-27) min for IPI 18-59 months and 16 (9-31) min for IPI 60-119 months (p=0.0014). Conclusions The second stage of labor did not differ in women with a prolonged IPI compared to normal multiparous women. Women with an IPI ≥120 months had a significantly longer second stage vs. those with a shorter IPI. These findings provide a better understanding of labor progression in pregnancies with a prolonged IPI.

LSTrAP-Cloud: A User-Friendly Cloud Computing Pipeline to Infer Coexpression Networks.

As genomes become more and more available, gene function prediction presents itself as one of the major hurdles in our quest to extract meaningful information on the biological processes genes participate in. In order to facilitate gene function prediction, we show how our user-friendly pipeline, the Large-Scale Transcriptomic Analysis Pipeline in Cloud (LSTrAP-Cloud), can be useful in helping biologists make a shortlist of genes involved in a biological process that they might be interested in, by using a single gene of interest as bait. The LSTrAP-Cloud is based on Google Colaboratory, and provides user-friendly tools that process quality-control RNA sequencing data streamed from the European Nucleotide Archive. The LSTRAP-Cloud outputs a gene coexpression network that can be used to identify functionally related genes for any organism with a sequenced genome and publicly available RNA sequencing data. Here, we used the biosynthesis pathway of Nicotiana tabacum as a case study to demonstrate how enzymes, transporters, and transcription factors involved in the synthesis, transport, and regulation of nicotine can be identified using our pipeline.

Placenta accreta: diagnosis, management and the molecular biology of the morbidly adherent placenta.

Placenta accreta is now the chief cause of postpartum hemorrhage resulting in maternal and neonatal morbidity. Prenatal diagnosis decreases blood loss at delivery and intra and post-partum complications. Ultrasound is critical for diagnosis and MRI is a complementary tool when the diagnosis is uncertain. Peripartum hysterectomy has been the standard of therapy but conservative management is increasingly being used. The etiology of accreta is due to a deficiency of maternal decidua resulting in placental invasion into the uterine myometrium. The molecular basis for the development of invasive placentation is yet to be elucidated but may involve abnormal paracrine/autocrine signaling between the deficient maternal decidua and the trophoblastic tissue. The interaction of hormones such as Relaxin which is abundant in maternal decidua and insulin-like 4, an insulin-like peptide found in placental trophoblastic tissue may play role in the formation of placenta accreta.

Placental profiling of UGT1A enzyme expression and activity and interactions with preeclampsia at term.

Placental UDP-glucuronosyltransferase (UGT) enzymes have critical roles in hormone, nutrient, chemical balance and fetal exposure during pregnancy. Placental UGT1A isoforms were profiled and differences between preeclamptic (PE) and non-PE placental UGT expression determined. In third trimester villous placenta, UGT1A1, 1A4, 1A6 and 1A9 were expressed and active in all specimens (n = 10), but UGT1A3, 1A5, 1A7, 1A8 and 1A10 were absent. The UGT1A activities were comparable to human liver microsomes per milligram, but placental microsome yields were only 2 % of liver (1 mg/g of tissue vs. 45 mg/g of tissue). For successful PCR, placental collection and processing within 60 min from delivery, including DNAse and ≥300 ng of RNA in reverse transcription were essential and snap freezing in liquid nitrogen immediately was the best preservation method. Although UGT1A6 mRNA was lower in PE (P < 0.001), there were no other significant effects on UGT mRNA, protein or activities. A more comprehensive tissue sample set is required for confirmation of PE interactions with UGT. Placental UGT1A enzyme expression patterns are similar to the liver and a detoxicative role for placental UGT1A is inferred.

Management of the adnexal mass in pregnancy.

PURPOSE OF REVIEW: With the increased use of ultrasonography in the first trimester, up to 1% of all pregnancies are diagnosed with an adnexal mass. Yet, the management of asymptomatic adnexal masses in pregnancy continues to be controversial as management guidelines are mainly based on case-control or observational studies. The purpose of this article was to review the recent literature and provide clinical guidance on patient management. RECENT FINDINGS: This review will highlight the increasing sensitivity of ultrasound imaging in diagnosing the rare malignant lesion, allowing for antenatal expectant management of benign asymptomatic adnexal masses until delivery or postpartum. The recent literature also highlights the well tolerated use of laparoscopy for the antenatal removal of suspicious or symptomatic masses and that expectant management of asymptomatic masses does not increase the risk of adverse pregnancy outcomes. SUMMARY: Most adnexal masses are benign and ultrasound characteristics can help guide the assessment of asymptomatic ovarian masses. When surgical management is chosen, laparoscopy can be safely performed in pregnancy. Ovarian torsion is a complication for persistent masses in pregnancy.

Hemoglobin A1c in pregestational diabetic gravidas and the risk of congenital heart disease in the fetus.

This study aimed to determine whether poor glycemic control in early pregnancy is associated with an increased risk of congenital heart disease (CHD) for infants of women with preexisting diabetes. A retrospective review examined two tertiary care centers of diabetic pregnancies that recorded early hemoglobin A1c (HbA1c) values (<20 weeks). The incidence of prenatally diagnosed CHD was calculated and stratified by HbA1c level. Poor glycemic control was defined as an HbA1c level of 8.5 % or higher. Fetal echocardiography was used to identify fetuses that resulted in infants with suspected CHD. Neonatal echocardiograms and pathology reports were reviewed for confirmation of the diagnosis. Of 535 patients, 30 (5.6 %) delivered an infant with confirmed CHD. Among the patients with poor glycemic control, 8.3 % (n = 17) delivered an infant with CHD, whereas 3.9 % (n = 13) of those with an HbA1c level lower than 8.5 % delivered an infant with CHD (p = 0.03). Poor glycemic control in early pregnancy is associated with an increased risk of CHD in offspring. The incidence of CHD in patients with adequate glycemic control still is sufficiently high to justify routine fetal echocardiography for all gravidas with preexisting diabetes regardless of HbA1c level.

Persistent ovarian masses and pregnancy outcomes.

OBJECTIVE: To determine if persistent ovarian masses in pregnancy are associated with increased adverse outcomes. METHODS: This is a retrospective cohort of 126 pregnant women with a persistent ovarian mass measuring 5 cm or greater who delivered at two university hospitals between 2001 and 2009. Maternal outcomes included gestational age (GA) at diagnosis, delivery and surgery as well as miscarriage, preterm birth (PTB), ovarian torsion and hospital admission for pain. Neonatal outcomes included birth weight, respiratory distress syndrome (RDS), intra-ventricular hemorrhage (IVH), death and sepsis. RESULTS: A total of 1225 ovarian masses were identified (4.9%) in 24,868 patients. A persistent ovarian mass was found in 0.7%. Average GA at diagnosis was 17.8 weeks. Miscarriage rate was 3.3%. Average GA at delivery was 37.9 weeks. Of the patients, 8.5% had ovarian torsion, 10.3% had admission for pain and 9.3% had PTBs. The mean cesarean delivery rate was 46.3%. The average neonatal weight was 3273 g. There was one neonatal death in this cohort. The rate of RDS was 2.8%, IVH 0.9% and neonatal sepsis 1.9%. The most common surgical pathologic diagnosis was dermoids (37.6%). No overt malignancies were seen. CONCLUSION: A persistent ovarian mass in pregnancy does not confer an increased risk of adverse pregnancy outcomes.

Relaxin, its receptor (RXFP1), and insulin-like peptide 4 expression through gestation and in placenta accreta.

This study was designed to show whether placental relaxin (RLN), its receptor (RXFP1), or insulin-like peptide 4 (INSL4) might have altered expression in patients with placenta accreta. The baseline expression of their genes through gestation (n = 34) was quantitated in the placental basal plate (BP) and villous trophoblast (TR), and compared to their expression in placenta accreta (n = 6). The proteins were also immunolocalized and quantitated in the accreta tissues. The messenger RNAs (mRNAs) of matrix metalloproteinase 9, -2, and tissue inhibitors of matrix metalloproteinase (TIMP)-1 were also measured. Results demonstrated that the BP and TR expressed low levels of RLN/RXFP1 and INSL4 through gestation. In accreta, increased RLN gene and protein in BP were associated with antepartum bleeding whereas INSL4 expression decreased throughout the TR. There were no changes in mRNAs for MMPs, but TIMP-1 was increased only in the invasive TR.

Physical activity before and during pregnancy and duration of second stage of labor among Hispanic women.

OBJECTIVE: To study a possible association between physical activity and the duration of second stage of labor among Hispanic women. STUDY DESIGN: We evaluated this relationship in the Latina Gestational Diabetes Mellitus Study, a prospective cohort of Hispanic obstetric patients. The Kaiser Physical Activity Survey was used to collect information on physical activity in prepregnancy, early pregnancy and mid-pregnancy. Duration of labor was abstracted from medical records. A total of 725 women with a singleton pregnancy and a spontaneous vaginal delivery were included, which yielded > 80% power to detect a clinically meaningful mean difference of 30 minutes. RESULTS: The mean duration of second-stage of labor was 34.3 min (SD 42.02). After adjusting for established risk factors, no significant differences in duration of labor were observed among women according to physical activity level in prepregnancy, early pregnancy, or midpregnancy. CONCLUSION: Findings confirm prior literature demonstrating the absence of an association between physical activity and duration of labor.