A systematic analysis of regression models for protein engineering.

To optimize proteins for particular traits holds great promise for industrial and pharmaceutical purposes. Machine Learning is increasingly applied in this field to predict properties of proteins, thereby guiding the experimental optimization process. A natural question is: How much progress are we making with such predictions, and how important is the choice of regressor and representation? In this paper, we demonstrate that different assessment criteria for regressor performance can lead to dramatically different conclusions, depending on the choice of metric, and how one defines generalization. We highlight the fundamental issues of sample bias in typical regression scenarios and how this can lead to misleading conclusions about regressor performance. Finally, we make the case for the importance of calibrated uncertainty in this domain.

Hematocrit control and thrombotic risk in patients with polycythemia vera treated with ruxolitinib in clinical practice.

Polycythemia vera (PV) is a myeloproliferative neoplasm characterized by unregulated red blood cell production resulting in elevated hemoglobin and/or hematocrit levels. Patients often have symptoms such as fatigue, pruritus, and painful splenomegaly, but are also at risk of thrombosis, both venous and arterial. Ruxolitinib, a selective Janus kinase inhibitor, is approved by the US Food and Drug Administration as second-line cytoreductive treatment after intolerance or inadequate response to hydroxyurea. Although ruxolitinib has been widely used in this setting, limited data exist in the literature on ruxolitinib treatment patterns and outcomes among patients with PV in routine clinical practice. We report a retrospective, observational, cohort study of patients treated for PV with ruxolitinib across three US centers (academic and regional practice) from December 2014-December 2019. The study included 69 patients, with a median follow-up duration of 3.7 years (95% CI, 2.9-4.4). Our data demonstrate very high rates of hematocrit control (88% of patients by three months and 89% by six months); few patients required dose adjustments or suspension. No arterial thromboses were observed; however, the follow-up duration does not allow for the generation of meaningful conclusions from this. Three patients had thrombotic events; one was in the setting of a second malignancy, one post-operative, and a third related to prolonged immobility. We also found that 28% of patients initiated ruxolitinib as a result of poorly controlled platelet counts, second only to hydroxyurea intolerance (46%) as a reason to start therapy. In clinical practice, ruxolitinib continues to be effective in controlling hematocrit levels after three and six months of treatment in patients and is associated with low thrombotic risk.

Characterization of recombinant phytase of Klebsiella sp. and the influence of novel 3-phytase on mineral solubility in broiler diets under an in vitro digestion assay.

Phytate (inositol hexaphosphate) is the major storage form of phosphorus (P) in nature, and phytases catalyze the hydrolysis of P from phytate and the formation of inositol phosphate isomers. In this study, a bacterium that produces phytase was isolated in a phytase screening medium. The bacterium was identified as Klebsiella sp. using phenotypic and molecular techniques. The PhyK phytase gene was successfully amplified from the genome, inserted into the pET-21a (+) vector, and expressed as a recombinant protein in E. Coli BL21. The efficiency of a laboratory phytase (Lab-Ph, PhyK phytase) was determined and compared with a commercial phytase (Com-Ph, Quantum Blue 40P phytase, AB Vista) under an in vitro digestion assay. The native signal peptide effectively facilitated the translocation of the protein to the periplasmic space of E. Coli BL21, resulting in the proper folding of the protein and the manifestation of desirable enzyme activity. The Lab-Ph displayed the temperature and pH optima at 50 °C and 5 respectively. In addition, the Lab-Ph was inactivated at 80 °C. Under an in vitro digestion assay condition, Lab-Ph improved the P solubility coefficient in broiler diets. In comparison, the Com-Ph significantly increased the P solubility coefficient even when compared with the Lab-Ph. In summary, this study has shown that Lab-Ph possesses the necessary biochemical properties to be used in various industrial applications. However, Lab-Ph is extremely sensitive to heat treatment. The Lab-Ph and Com-Ph under an in vitro digestion assay improved the solubility coefficient of P in the broiler diet.

Periportal necrosis and successful liver transplantation following Lamotrigine drug-induced liver injury in a child.

Lamotrigine is one of the most prescribed antiepileptics in children and a well-known cause of drug-induced liver injury (DILI). The typical presentation usually includes a drug rash with eosinophilia and systemic symptoms (DRESS syndrome). Cases are typically mild and self-limiting, requiring supportive care only. We report a severe Lamotrigine-induced DILI with a non-typical presentation with hyperammonaemia and rapid clinical deterioration. We present a literature review exploring contributing factors, transplant considerations and liver histology. Histology showed periportal necrosis, which is recognised as a pattern of DILI but has not been previously described with Lamotrigine. Our patient proceeded to transplant and is the first reported liver transplant for Lamotrigine DILI in a child. A directed and rapid diagnostic approach is crucial to avoid delays and rule out multisystemic metabolic and genetic conditions that preclude liver transplantation.

Confirming Silent Translocation through Nanopores with Simultaneous Single-Molecule Fluorescence and Single-Channel Electrical Recordings.

Most of what is known concerning the luminal passage of materials through nanopores arises from electrical measurements. Whether nanopores are biological, solid-state, synthetic, hybrid, glass-capillary-based, or protein ion channels in cells and tissues, characteristic signatures embedded in the flow of ionic current are foundational to understanding functional behavior. In contrast, this work describes passage through a nanopore that occurs without producing an electrical signature. We refer to the phenomenon as "silent translocation." By definition, silent translocations are invisible to the standard tools of electrophysiology and fundamentally require a simultaneous ancillary measurement technique for positive identification. As a result, this phenomenon has been largely unexplored in the literature. Here, we report on a derivative of Cyanine 5 (sCy5a) that passes through the α-hemolysin (αHL) nanopore silently. Simultaneously acquired single-molecule fluorescence and single-channel electrical recordings from bilayers formed over a closed microcavity demonstrate that translocation does indeed take place, albeit infrequently. We report observations of silent translocation as a function of time, dye concentration, and nanopore population in the bilayer. Lastly, measurement of the translocation rate as a function of applied potential permits estimation of an effective energy barrier for transport through the pore as well as the effective charge on the dye, all in the absence of an information-containing electrical signature.

Unbiased discovery of natural sequence variants that influence fungal virulence.

Isolates of Cryptococcus neoformans, a fungal pathogen that kills over 112,000 people each year, differ from a 19-Mb reference genome at a few thousand up to almost a million DNA sequence positions. We used bulked segregant analysis and association analysis, genetic methods that require no prior knowledge of sequence function, to address the key question of which naturally occurring sequence variants influence fungal virulence. We identified a region containing such variants, prioritized them, and engineered strains to test our findings in a mouse model of infection. At one locus, we identified a 4-nt variant in the PDE2 gene that occurs in common laboratory strains and severely truncates the encoded phosphodiesterase. The resulting loss of phosphodiesterase activity significantly impacts virulence. Our studies demonstrate a powerful and unbiased strategy for identifying key genomic regions in the absence of prior information and provide significant sequence and strain resources to the community.

Approaches to determine the efficiency of novel 3-phytase from Klebsiella pneumoniae and commercial phytase in broilers from 1 to 14 d of age.

This study aimed to evaluate the effects of a laboratory 3-phytase (the expression of the phyK gene, Lab-Phy) and a commercial 6-phytase (Quantum Blue 40 P, Com-Phy) alone and in combination (corn-soy-based diets) in broilers. A total of 400, day-old Ross 308 male broilers were randomly assigned to 5 treatments with 10 replicate cages (8 chicks/cage) for a 14-day trial. Experimental treatments included the positive control (0.95% Ca and 0.48% nonphytate phosphorus (nPP), PC), negative control (0.90% Ca and 0.22% nPP, NC), and NC which was supplemented with Lab-Phy 250 FTU/kg and Com-Phy 250 FTU/kg alone or in combination of Lab-Phy 125 FTU/kg and Com-Phy 125 FTU/kg. The inclusion of Lab-Phy in the NC diet significantly improved the P and Ca content in the tibia compared to the NC group. Moreover, the inclusion of Com-Phy alone and in combination with Lab-Phy in the NC diet significantly increased the P and Ca content in the tibia compared to the Lab-Phy. The mRNA expression of NaPi-IIb was upregulated in the duodenum by the reduction of nPP and downregulated by the inclusion of any phytase, whereas other nutrient transporters were not influenced by the reduction of nPP or the addition of phytase in the small intestine mucosa. Broilers receiving the NC diet obtained the lowest body weight (BW) and body weight gain (BWG) at 8 to 14 and 1 to 14 d of age. The NC group showed the lowest villi height and surface area, Newcastle disease (ND) antibody titer, and digestibility of nutrients compared to the PC group at 14 d of age. Supplementing the NC diet with the Lab-Phy and Com-Phy individually, or in combination tended to improve BW, BWG, tibia characteristics, villi characteristics, ND, and retained CP and P, and apparent ileal digestibility of CP, P, methionine, and threonine. The present research indicated that the studied traits by the combination of phytases were slightly better than the average of the 2 individually, suggesting there might be some value in combining the laboratory and commercial phytases.

A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets.

The CRISPR/Cas9 nuclease from Streptococcus pyogenes (SpCas9) can be used with single guide RNAs (sgRNAs) as a sequence-specific antimicrobial agent and as a genome-engineering tool. However, current bacterial sgRNA activity models struggle with accurate predictions and do not generalize well, possibly because the underlying datasets used to train the models do not accurately measure SpCas9/sgRNA activity and cannot distinguish on-target cleavage from toxicity. Here, we solve this problem by using a two-plasmid positive selection system to generate high-quality data that more accurately reports on SpCas9/sgRNA cleavage and that separates activity from toxicity. We develop a machine learning architecture (crisprHAL) that can be trained on existing datasets, that shows marked improvements in sgRNA activity prediction accuracy when transfer learning is used with small amounts of high-quality data, and that can generalize predictions to different bacteria. The crisprHAL model recapitulates known SpCas9/sgRNA-target DNA interactions and provides a pathway to a generalizable sgRNA bacterial activity prediction tool that will enable accurate antimicrobial and genome engineering applications.

An Electrochemical Approach to Directed Fluorination.

Electrosynthesis has made a revival in the field of organic chemistry and, in particular, radical-mediated reactions. Herein, we report a simple directed, electrochemical C-H fluorination method. Employing a dabconium mediator, commercially available Selectfluor, and RVC electrodes, we provide a range of steroid-based substrates with competent regioselective directing groups, including enones, ketones, and hydroxy groups, as well as never reported before lactams, imides, lactones, and esters.

Physical properties and biological effects of ceramic materials emitting infrared radiation for pain, muscular activity, and musculoskeletal conditions.

BACKGROUND: Up to 33% of the general population worldwide suffer musculoskeletal conditions, with low back pain being the single leading cause of disability globally. Multimodal therapeutic options are available to relieve the pain associated with muscular disorders, including physical, complementary, and pharmacological therapies. However, existing interventions are not disease modifying and have several limitations. METHOD: Literature review. RESULTS: In this context, the use of nonthermal infrared light delivered via patches, fabrics, and garments containing infrared-emitting bioceramic minerals have been investigated. Positive effects on muscular cells, muscular recovery, and reduced inflammation and pain have been reported both in preclinical and clinical studies. There are several hypotheses on how infrared may contribute to musculoskeletal pain relief, however, the full mechanism of action remains unclear. This article provides an overview of the physical characteristics of infrared radiation and its biological effects, focusing on those that could potentially explain the mechanism of action responsible for the relief of musculoskeletal pain. CONCLUSIONS: Based on the current evidence, the following pathways have been considered: upregulation of endothelial nitric oxide synthase, increase in nitric oxide bioavailability, anti-inflammatory effects, and reduction in oxidative stress.

Imaging of pediatric extremity soft tissue tumors: A COG Diagnostic Imaging Committee/SPR Oncology Committee White Paper.

Pediatric soft tissue tumors of the extremity include rhabdomyosarcoma and nonrhabdomyosarcoma neoplasms. This manuscript provides consensus-based imaging recommendations for imaging evaluation at diagnosis, during treatment, and following completion of therapy for patients with a soft tissue tumor of the extremity.

C-F Bonds as "Frozen" Nucleophiles: Unconsummated SN2 Reactions.

In this note, we present a series of rigid molecules that show close enforced interactions between Ar-F moieties and -CH2X groups in a "tetrel bond" configuration similar to a nascent SN2 attack. We explore the spectroscopic, crystallographic, and chemical reactivity consequences of these unusual interactions, including significant through-space spin-spin couplings, short C-F···CH2X distances, and differential SN1 and SN2 reaction pathways. We also reveal experimental evidence of carbon-based tetrel bonds influencing chemical reactivity in solution. Finally, density functional theory (DFT) calculations are employed throughout this study to confirm and illuminate our experimental data.

Utilizing prospective space-time scan statistics to discover the dynamics of coronavirus disease 2019 clusters in the State of São Paulo, Brazil.

BACKGROUND: The number of deaths and people infected with coronavirus disease 2019 (COVID-19) in Brazil has steadily increased in the first few months of the pandemic. Despite the underreporting of coronavirus cases by government agencies across the country, São Paulo has the highest rate among all Brazilian states. METHODS: To identify the highest-risk municipalities during the initial outbreak, we utilized daily confirmed case data from official reports between February 25 and May 5, 2020, which were aggregated to the municipality level. A prospective space-time scan statistic was conducted to detect active clusters in three different time periods. RESULTS: Our findings suggest that approximately 4.6 times more municipalities belong to a significant space-time cluster with a relative risk (RR) > 1 on May 5, 2020. CONCLUSIONS: Our study demonstrated the applicability of the space-time scan statistic for the detection of emerging clusters of COVID-19. In particular, we identified the clusters and RR of municipalities in the initial months of the pandemic, explaining the spatiotemporal patterns of COVID-19 transmission in the state of São Paulo. These results can be used to improve disease monitoring and facilitate targeted interventions.

Hydroxy-directed fluorination of remote unactivated C(sp3)-H bonds: a new age of diastereoselective radical fluorination.

We report a photochemically induced, hydroxy-directed fluorination that addresses the prevailing challenge of high diastereoselectivity in this burgeoning field. Numerous simple and complex motifs showcase a spectrum of regio- and stereochemical outcomes based on the configuration of the hydroxy group. Notable examples include a long-sought switch in the selectivity of the refractory sclareolide core, an override of benzylic fluorination, and a rare case of 3,3'-difluorination. Furthermore, calculations illuminate a low barrier transition state for fluorination, supporting our notion that alcohols are engaged in coordinated reagent direction. A hydrogen bonding interaction between the innate hydroxy directing group and fluorine is also highlighted for several substrates with 19F-1H HOESY experiments, calculations, and more.

Prospective study of factors associated with asthma attack recurrence (ATTACK) in children from three Ecuadorian cities during COVID-19: a study protocol.

INTRODUCTION: Asthma is a growing health problem in children in marginalised urban settings in low-income and middle-income countries. Asthma attacks are an important cause of emergency care attendance and long-term morbidity. We designed a prospective study, the Asthma Attacks study, to identify factors associated with recurrence of asthma attacks (or exacerbations) among children and adolescents attending emergency care in three Ecuadorian cities. METHODS AND ANALYSIS: Prospective cohort study designed to identify risk factors associated with recurrence of asthma attacks in 450 children and adolescents aged 5-17 years attending emergency care in public hospitals in three Ecuadorian cities (Quito, Cuenca and Portoviejo). The primary outcome will be rate of asthma attack recurrence during up to 12 months of follow-up. Data are being collected at baseline and during follow-up by questionnaire: sociodemographic data, asthma history and management (baseline only); recurrence of asthma symptoms and attacks (monthly); economic costs of asthma to family; Asthma Control Test; Pediatric Asthma Quality of life Questionnaire; and Newcastle Asthma Knowledge Questionnaire (baseline only). In addition, the following are being measured at baseline and during follow-up: lung function and reversibility by spirometry before and after salbutamol; fractional exhaled nitric oxide (FeNO); and presence of IgG antibodies to SARS-CoV-2 in blood. Recruitment started in 2019 but because of severe disruption to emergency services caused by the COVID-19 pandemic, eligibility criteria were modified to include asthmatic children with uncontrolled symptoms and registered with collaborating hospitals. Data will be analysed using logistic regression and survival analyses. ETHICS AND DISSEMINATION: Ethical approval was obtained from the Hospital General Docente de Calderon (CEISH-HGDC 2019-001) and Ecuadorian Ministry of Public Health (MSP-CGDES-2021-0041-O N° 096-2021). The study results will be disseminated through presentations at conferences and to key stakeholder groups including policy-makers, postgraduate theses, peer-review publications and a study website. Participants gave informed consent to participate in the study before taking part.

The Close Interaction of a C-F Bond with an Amide Carbonyl: Crystallographic and Spectroscopic Characterization.

The putative interaction of a C-F bond with an amide carbonyl has been an intriguing topic of interest in this century for reasons spanning basic physical organic chemistry to biochemistry. However, to date, there exist no examples of a close, well-defined interaction in which its unique aspects can be identified and exploited. Herein, we finally present an engineered system possessing an exceptionally tight C-F-amide interaction, allowing us to obtain spectroscopic, crystallographic, and kinetic details of a distinctive, biochemically relevant chemical system for the first time. In turn, we also explore Lewis acid coordination, C-F bond promotion of amide isomerization, enantiomerization, and ion protonation processes.

Paediatric Gastrointestinal, Hepatic and Pancreatic Inflammatory Myofibroblastic Tumours, A Single Centre Experience.

ABSTRACT: Inflammatory myofibroblastic tumours (IMTs) are rare soft tissue tumours. Reports of gastrointestinal tract, liver and pancreas tumours are limited. The objective of this study is to identify presenting features, contributing prognostic / etiological factors and any variability in outcomes in the context of different historical treatments. We retrospectively reviewed the records of seven children treated at our hospital between 2006 and 2019 and assessed the demographic, presentation, treatment, immunohistochemistry, and outcomes of their tumours. Age range at presentation was 4 months-15 years with a male predominance. Presentations were typically due to local mass effect or incidental discovery. Systemic symptoms were rare. Outcomes were good with six out of seven stable or in remission irrespective of treatment. Surgical resection where possible is the treatment of choice. Medical therapy had good outcomes with chemotherapy acting as first line treatment when required. The only negative prognostic factor identified was local spread at the time of presentation.

Utilizing prospective space-time scan statistics to discover the dynamics of coronavirus disease 2019 clusters in the State of São Paulo, Brazil

ABSTRACT Background: The number of deaths and people infected with coronavirus disease 2019 (COVID-19) in Brazil has steadily increased in the first few months of the pandemic. Despite the underreporting of coronavirus cases by government agencies across the country, São Paulo has the highest rate among all Brazilian states. Methods: To identify the highest-risk municipalities during the initial outbreak, we utilized daily confirmed case data from official reports between February 25 and May 5, 2020, which were aggregated to the municipality level. A prospective space-time scan statistic was conducted to detect active clusters in three different time periods. Results: Our findings suggest that approximately 4.6 times more municipalities belong to a significant space-time cluster with a relative risk (RR) > 1 on May 5, 2020. Conclusions: Our study demonstrated the applicability of the space-time scan statistic for the detection of emerging clusters of COVID-19. In particular, we identified the clusters and RR of municipalities in the initial months of the pandemic, explaining the spatiotemporal patterns of COVID-19 transmission in the state of São Paulo. These results can be used to improve disease monitoring and facilitate targeted interventions.

Obesity and revision surgery, mortality, and patient-reported outcomes after primary knee replacement surgery in the National Joint Registry: A UK cohort study.

BACKGROUND: One in 10 people in the United Kingdom will need a total knee replacement (TKR) during their lifetime. Access to this life-changing operation has recently been restricted based on body mass index (BMI) due to belief that high BMI may lead to poorer outcomes. We investigated the associations between BMI and revision surgery, mortality, and pain/function using what we believe to be the world's largest joint replacement registry. METHODS AND FINDINGS: We analysed 493,710 TKRs in the National Joint Registry (NJR) for England, Wales, Northern Ireland, and the Isle of Man from 2005 to 2016 to investigate 90-day mortality and 10-year cumulative revision. Hospital Episodes Statistics (HES) and Patient Reported Outcome Measures (PROMs) databases were linked to the NJR to investigate change in Oxford Knee Score (OKS) 6 months postoperatively. After adjustment for age, sex, American Society of Anaesthesiologists (ASA) grade, indication for operation, year of primary TKR, and fixation type, patients with high BMI were more likely to undergo revision surgery within 10 years compared to those with "normal" BMI (obese class II hazard ratio (HR) 1.21, 95% CI: 1.10, 1.32 (p < 0.001) and obese class III HR 1.13, 95% CI: 1.02, 1.26 (p = 0.026)). All BMI classes had revision estimates within the recognised 10-year benchmark of 5%. Overweight and obese class I patients had lower mortality than patients with "normal" BMI (HR 0.76, 95% CI: 0.65, 0.90 (p = 0.001) and HR 0.69, 95% CI: 0.58, 0.82 (p < 0.001)). All BMI categories saw absolute increases in OKS after 6 months (range 18-20 points). The relative improvement in OKS was lower in overweight and obese patients than those with "normal" BMI, but the difference was below the minimal detectable change (MDC; 4 points). The main limitations were missing BMI particularly in the early years of data collection and a potential selection bias effect of surgeons selecting the fitter patients with raised BMI for surgery. CONCLUSIONS: Given revision estimates in all BMI groups below the recognised threshold, no evidence of increased mortality, and difference in change in OKS below the MDC, this large national registry shows no evidence of poorer outcomes in patients with high BMI. This study does not support rationing of TKR based on increased BMI.