Miracle-dz/UniFAR-FTUs huggingface dataset:
An Arabidopsis expression predictor enables inference of transcriptional regulators for gene modules.

The regulation of gene expression by transcription factors (TF) has been studied for long, but no model that can accurately predict transcriptome profiles based on TF activities currently exists. Here, we developed a computational approach, named EXPLICIT, to construct a universal predictor for Arabidopsis to predict the expression of 29,182 non-TF genes using 1,678 TFs. When applied to RNA-Seq samples from diverse tissues, EXPLICIT generated accurate predicted transcriptomes correlating well with actual expression, with an average correlation coefficient of 0.986. After recapitulating the quantitative relationships between TFs and their target genes, EXPLICIT enabled downstream inference of TF regulators for genes and gene modules functioning in diverse plant pathways, including those involved in suberin, flavonoid, glucosinolate metabolism, lateral root, xylem, secondary cell wall development, or endoplasmic reticulum stress response. Our approach showed a better ability to recover the correct TF regulators when compared to existing plant tools, and provides an innovative way to study transcriptional regulation. SUPPORTING INFORMATION.
Carceral-community epidemiology, structural racism, and COVID-19 disparities

Significance As jails and prisons remain leading sites of COVID-19 outbreaks, mass incarceration poses ongoing health risks for communities. We investigate whether short-term jailing of individuals prior to release may drive COVID-19 spread. We find that cycling individuals through Cook County Jail in March 2020 alone can account for 13% of all COVID-19 cases and 21% of racial COVID-19 disparities in Chicago as of early August. We conclude that detention for alleged offenses that can be safely managed without incarceration is likely harming public safety and driving racial health disparities. These findings reinforce consensus among public health experts that large-scale decarceration should be implemented to protect incarcerated people, mitigate disease spread and racial disparities, and improve biosecurity and pandemic preparedness. Black and Hispanic communities are disproportionately affected by both incarceration and COVID-19. The epidemiological relationship between carceral facilities and community health during the COVID-19 pandemic, however, remains largely unexamined. Using data from Cook County Jail, we examine temporal patterns in the relationship between jail cycling (i.e., arrest and processing of individuals through jails before release) and community cases of COVID-19 in Chicago ZIP codes. We use multivariate regression analyses and a machine-learning tool, elastic regression, with 1,706 demographic control variables. We find that for each arrested individual cycled through Cook County Jail in March 2020, five additional cases of COVID-19 in their ZIP code of residence are independently attributable to the jail as of August. A total 86% of this additional disease burden is borne by majority-Black and/or -Hispanic ZIPs, accounting for 17% of cumulative COVID-19 cases in these ZIPs, 6% in majority-White ZIPs, and 13% across all ZIPs. Jail cycling in March alone can independently account for 21% of racial COVID-19 disparities in Chicago as of August 2020. Relative to all demographic variables in our analysis, jail cycling is the strongest predictor of COVID-19 rates, considerably exceeding poverty, race, and population density, for example. Arrest and incarceration policies appear to be increasing COVID-19 incidence in communities. Our data suggest that jails function as infectious disease multipliers and epidemiological pumps that are especially affecting marginalized communities. Given disproportionate policing and incarceration of racialized residents nationally, the criminal punishment system may explain a large proportion of racial COVID-19 disparities noted across the United States.
The Relationships of Nursing Home Culture Change Practices With Resident Quality of Life and Family Satisfaction: Toward a More Nuanced Understanding

Transforming nursing homes (NHs) from restrictive institutions to person-centered homes, referred to as NH culture change, is complex and multifaceted. This study, based on a survey of administrators in Minnesota NHs (n = 102), tested the domain-specific relationships of culture change practices with resident quality of life (QOL) and family satisfaction, and examined the moderating effect of small-home or household models on these relationships. The findings revealed that culture change operationalized through physical environment transformation, staff empowerment, staff leadership, and end-of-life care was positively associated with at least one domain of resident QOL and family satisfaction, while staff empowerment had the most extensive effects. Implementing small-home and household models had a buffering effect on the positive relationships between staff empowerment and the outcomes. The findings provide meaningful implications for designing and implementing NH culture change practices that best benefit residents’ QOL and improve family satisfaction.
Differential spatiotemporal development of Purkinje cell populations and cerebellum-dependent sensorimotor behaviors

Distinct populations of Purkinje cells (PCs) with unique molecular and connectivity features are at the core of the modular organization of the cerebellum. Previously, we showed that firing activity of PCs differs between ZebrinII-positive and ZebrinII-negative cerebellar modules (Zhou et al., 2014; Wu et al., 2019). Here, we investigate the timing and extent of PC differentiation during development in mice. We found that several features of PCs, including activity levels, dendritic arborization, axonal shape and climbing fiber input, develop differentially between nodular and anterior PC populations. Although all PCs show a particularly rapid development in the second postnatal week, anterior PCs typically have a prolonged physiological and dendritic maturation. In line herewith, younger mice exhibit attenuated anterior-dependent eyeblink conditioning, but faster nodular-dependent compensatory eye movement adaptation. Our results indicate that specific cerebellar regions have unique developmental timelines which match with their related, specific forms of cerebellum-dependent behaviors.
"Just Engage in It or Not, You Get Out What You Put In": Student and Staff Experiences of Feedback and Feedforward in Workplace-Based Learning Environments.

Feedback is central to student learning in the veterinary workplace. Feedforward, a related concept, is used to describe the way information about a student's performance may be used to improve their future performance. Feedback and feedforward practices are diverse, with varied student and staff understandings of the nature and purpose of feedback (feedback literacy). This study compared the practices of feedback and feedforward in a range of programs in one institution during student transitions from the classroom to workplace-based learning environments. The study adopted a broad inter-professional approach to include health care programs as well as social work and theater and performance studies. Profession-specific focus groups were conducted with contribution from 28 students and 31 staff from five different professions. Thematic analysis revealed that students and staff shared an understanding of the feedback and feedforward concepts, and both groups recognized the importance of emotional and relational aspects of the process. Students and staff across all professions recognized the impact of time constraints on the feedback process, although this was particularly highlighted in the health science professions. Social work and theater and performance studies students demonstrated a more nuanced understanding of the emotional and relational aspects of feedback and feedforward. Overall, the approach highlights similarities and differences in practices and experiences in different workplace contexts, creating opportunities for cross-disciplinary learning, which may have relevance more widely in higher education programs with workplace-based elements. The study underpinned the development of the LeapForward feedback training resource (https://bilt.online/the-leapforward-project/).
Early Discrimination Between Tumor‐Induced Rickets/Osteomalacia and X‐Linked Hypophosphatemia in Chinese Children and Adolescents: A Retrospective Case–Control Study

In children and adolescents, distinguishing tumor‐induced rickets/osteomalacia (TIR/O) from hereditary hypophosphatemic rickets/osteomalacia (HR/O) is a medical challenge. We retrospectively studied 10 Chinese children and adolescents with TIR/O who underwent surgery at a mean age of 17.4 ± 2.1 years and compared their characteristics to 24 age‐ and sex‐matched patients with X‐linked hypophosphatemia (XLH). Positive family history of HR/O and dental problems, such as enamel hypoplasia and dental abscess, were reported in 8 (33.3%) and 5 (20.8%) patients with XLX, respectively, but not in patients with TIR/O. In addition, in comparison with XLH patients, TIR/O patients had an older disease onset age (150 versus 24 months, p < 0.001), a higher height standard deviation score (SDS; −1.2 ± 1.8 versus −4.0 ± 1.4, p < 0.001), a lower Z‐score of bone mineral density (BMD) at lumbar spine (LS) (−3.9 [6.0] versus +1.8 [7.0], p < 0.001), and a higher serum intact fibroblast growth factor 23 (FGF23) level (500.27 ± 87.20 versus 121.71 ± 70.94 pg/mL, p < 0.001), corresponding to a lower serum phosphate level (0.52 ± 0.07 versus 0.64 ± 0.11 mmol/L, p = 0.005) and a higher serum alkaline phosphatase (ALP) level (557 [631] versus 305 [249] U/L, p = 0.005). We generated receiver operating characteristic (ROC) curves and calculated the area under the ROC curve (AUC). The AUCs of onset age, FGF23, and LS Z‐score were equal to 1, suggesting that these are excellent indices for the differential diagnosis between TIR/O and XLH. In summary, our study furthers our understanding of the spectrum of clinical, biochemical, and pathologic findings associated with TIR/O. For children and adolescent patients with HR/O, a comprehensive and careful clinical and laboratory evaluation is of great importance, and we recommend enquiry of the family history, onset age, and dental problems, as well as measurement of serum FGF23 and BMD. © 2021 American Society for Bone and Mineral Research (ASBMR).
AlphaFold2 predicts the inward‐facing conformation of the multidrug transporter LmrP

As part of the CASP competition, the protein structure prediction algorithm AlphaFold2 generated multiple models of the proton/drug antiporter LmrP. Previous distance restraints from double electron‐electron resonance spectroscopy, a technique which reports distance distributions between spin labels attached to proteins, suggest that one of the lower‐ranked models may have captured a conformation that has so far eluded experimental structure determination.
Comparison of Optimized Isotherm Models and Error Functions for Carbon Dioxide Adsorption on Activated Carbon

The adsorption of CO2 on commercial activated carbon WG12 and WG12 modified by ZnCl2 and KOH was investigated using a high pressure Sievert’s apparatus. The experimental data were analyzed using Langmuir, Freundlich, Sips, Toth, Unilan, Ftitz–Schlunder, and Redlich–Peterson equations. An error analysis was performed to examine the effect of using different error criteria for the isotherm parameters determination. Five error analysis methods were used: the sum of the squares of errors, the hybrid fractional error function, the average relative error, the Marquardt’s percent standard deviation, and the sum of the absolute errors. The Sips isotherm provided the best quality of fitting for all the experimental data. Error function analysis found that sum of the squares of the errors and hybrid fractional error function provided the best overall results.
REMOVAL OF Cr (VI) FROM AQUEOUS SOLUTION USING PINE NEEDLES POWDER AS A BIOSORBENT

The removal of Cr (VI) from aqueous solution was performed using pine needles powder as a biosorbent by batch adsorption technique. The operating variables studied were adsorbent dose, particle size, agitation speed, pH of solution, contact time and initial Cr (VI) concentration. Adsorption process was found to be highly pH dependent. The optimum pH range for adsorption of Cr (VI) was found to be between 2 and 3. Adsorption isotherms were modeled with the Langmuir, Freundlich, Dubinin- Radushkevich and Tempkin isotherms. Langmuir equation is found to best represent the equilibrium data for Cr (VI) 0 pine needles powder system than other isotherms (R 2 = 0.9946). The maximum monolayer adsorption capacity was found to be 40.0 mg g 01 at 298K.
Deep Learning Model for Automated Detection and Classification of Central Canal, Lateral Recess, and Neural Foraminal Stenosis at Lumbar Spine MRI.

Background Assessment of lumbar spinal stenosis at MRI is repetitive and time consuming. Deep learning (DL) could improve -productivity and the consistency of reporting. Purpose To develop a DL model for automated detection and classification of lumbar central canal, lateral recess, and neural -foraminal stenosis. Materials and Methods In this retrospective study, lumbar spine MRI scans obtained from September 2015 to September 2018 were included. Studies of patients with spinal instrumentation or studies with suboptimal image quality, as well as postgadolinium studies and studies of patients with scoliosis, were excluded. Axial T2-weighted and sagittal T1-weighted images were used. Studies were split into an internal training set (80%), validation set (9%), and test set (11%). Training data were labeled by four radiologists using predefined gradings (normal, mild, moderate, and severe). A two-component DL model was developed. First, a convolutional neural network (CNN) was trained to detect the region of interest (ROI), with a second CNN for classification. An internal test set was labeled by a musculoskeletal radiologist with 31 years of experience (reference standard) and two subspecialist radiologists (radiologist 1: A.M., 5 years of experience; radiologist 2: J.T.P.D.H., 9 years of experience). DL model performance on an external test set was evaluated. Detection recall (in percentage), interrater agreement (Gwet κ), sensitivity, and specificity were calculated. Results Overall, 446 MRI lumbar spine studies were analyzed (446 patients; mean age ± standard deviation, 52 years ± 19; 240 women), with 396 patients in the training (80%) and validation (9%) sets and 50 (11%) in the internal test set. For internal testing, DL model and radiologist central canal recall were greater than 99%, with reduced neural foramina recall for the DL model (84.5%) and radiologist 1 (83.9%) compared with radiologist 2 (97.1%) (P < .001). For internal testing, dichotomous classification (normal or mild vs moderate or severe) showed almost-perfect agreement for both radiologists and the DL model, with respective κ values of 0.98, 0.98, and 0.96 for the central canal; 0.92, 0.95, and 0.92 for lateral recesses; and 0.94, 0.95, and 0.89 for neural foramina (P < .001). External testing with 100 MRI scans of lumbar spines showed almost perfect agreement for the DL model for dichotomous classification of all ROIs (κ, 0.95-0.96; P < .001). Conclusion A deep learning model showed comparable agreement with subspecialist radiologists for detection and classification of central canal and lateral recess stenosis, with slightly lower agreement for neural foraminal stenosis at lumbar spine MRI. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Hayashi in this issue.
Horizontal transfer of domains in ssrA gene among Enterobacteriaceae

The tmRNA (transfer messenger RNA), encoded by ssrA gene, is involved in rescuing of stalled ribosomes by a process called trans‐translation. Additionally, regions of the ssrA gene (coding for tmRNA) were reported to serve as integration sites for various bacteriophages. Though variations in ssrA genes were reported, their functional relevance is less studied. In this study, we investigated the horizontal gene transfer (HGT) of ssrA among the members of Enterobacteriaceae. This was done by predicting recombination signals in ssrA gene (belonging to Enterobacteriaceae) using RDP5 (Recombination Detection Program 5). Our results revealed 7 recombination signals in ssrA gene belonging to different species. We further showed that the recombination signals were more in the domains present in the 3′ end than 5′ end of tmRNA. Of note, the mRNA region was reported in many recombination signals. Further, members belonging to genera Yersinia, Erwinia, Dickeya and Enterobacter were highly represented in the recombination signals. Sequence analysis revealed the presence of integration sites for different class of bacteriophages in ssrA gene. The locations of phage recognition sites are comparable with recombination signals. Taken together, our results revealed a diverse nature of HGT and recombination which possibly due to transduction mediated by phages.
Antipsychotic treatment in clinical high risk for psychosis: Iatrogenesis related to dopamine supersensitivity psychosis?

1 Department of Psychiatry, Monash University, Clayton, VIC, Australia 2 College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia 3 Consortium of Australian-Academic Psychiatrists for Independent Policy and Research Analysis (CAPIPRA), Canberra, ACT, Australia 4 Department of Psychiatry, LKS Faculty of Medicine, University of Hong Kong, Hong Kong SAR 5 The State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong 6 Academic Unit of Psychiatry and Addiction Medicine, The Australian National University Medical School, Canberra Hospital, Canberra, ACT, Australia
Effect of an Internet-Delivered Stepped-Care Program vs In-Person Cognitive Behavioral Therapy on Obsessive-Compulsive Disorder Symptoms in Children and Adolescents: A Randomized Clinical Trial.

Importance In most countries, young people with obsessive-compulsive disorder have limited access to specialist cognitive behavioral therapy (CBT), a first-line treatment. Objective To investigate whether internet-delivered CBT implemented in a stepped-care model is noninferior to in-person CBT for pediatric obsessive-compulsive disorder. Design, Setting and Participants A randomized clinical noninferiority trial conducted at 2 specialist child and adolescent mental health clinics in Sweden. Participants included 152 individuals aged 8 to 17 years with obsessive-compulsive disorder. Enrollment began in October 2017 and ended in May 2019. Follow-up ended in April 2020. Interventions Participants randomized to the stepped-care group (n = 74) received internet-delivered CBT for 16 weeks. Nonresponders at the 3-month follow-up were then offered a course of traditional face-to-face treatment. Participants randomized to the control group (n = 78) immediately received in-person CBT for 16 weeks. Nonresponders at the 3-month follow-up received additional face-to-face treatment. Main Outcomes and Measures The primary outcome was the masked assessor-rated Children's Yale-Brown Obsessive-Compulsive Scale (CY-BOCS) score at the 6-month follow-up. The scale includes 10 items rated from 0 (no symptoms) to 4 (extreme symptoms), yielding a total score range of 0 to 40, with higher scores indicating greater severity. Assessors were masked to treatment allocation at pretreatment, posttreatment, 3-month follow-up, and 6-month follow-up assessments. The predefined noninferiority margin was 4 points on the CY-BOCS. Results Among the 152 randomized participants (mean age, 13.4 years; 94 [62%] females), 151 (99%) completed the trial. At the 3-month follow-up, 34 participants (46%) in the stepped-care group and 23 (30%) in the in-person CBT group were nonresponders. At the 6-month follow-up, the CY-BOCS score was 11.57 points in the stepped-care group vs 10.57 points in the face-to-face treatment group, corresponding to an estimated mean difference of 0.91 points ([1-sided 97.5% CI, -∞ to 3.28]; P for noninferiority = .02). Increased anxiety (30%-36%) and depressive symptoms (20%-28%) were the most frequently reported adverse events in both groups. There were 2 unrelated serious adverse events (1 in each group). Conclusions and Relevance Among children and adolescents with obsessive-compulsive disorder, treatment with an internet-delivered CBT program followed by in-person CBT if necessary compared with in-person CBT alone resulted in a noninferior difference in symptoms at the 6-month follow-up. Further research is needed to understand the durability and generalizability of these findings. Trial Registration ClinicalTrials.gov Identifier: NCT03263546.
Perioperative antibiotic prophylaxis in spinal surgery

Study design: Complete audit cycle. Introduction: To highlight the unjustified overuse of perioperative antibiotics in clean non-instrumented lumbar spinal surgeries. To convince orthopedic surgeons in a methodological way of local field comparison between common practice on the use of perioperative antibiotics prophylaxis (PAP) in clean non-instrumented lumbar spinal surgeries and the ideal practice according to “The guidelines published by North American Spine Society (NASS)”. Methods: A complete audit cycle had been done. One hundred and eight patients underwent clean non-instrumented lumbar spinal surgeries in a tertiary spine center, during the period from the 1st of April to the 31st of June 2017 (primary audit period) and during the period from the 8th of May to the 21st of November 2018 (re-audit period). Group I: audit group (n = 54) was given the usual regimen (IV first-generation cephalosporin for 1–6 days, followed by oral antibiotics, till the removal of stitches) and Group II: re-audit group (n = 54) received only the IV antibiotics for one day). The study protocol was approved by our institution’s Ethical Committee (17100582). Results: This study showed a wide gap between international standards and local prescribing practices and calls for multiple interventions to improve our practice. Out of the 108 patients, only one case (1.85%) developed surgical site infection (SSI) in the audit group (Group I). The difference in infection rates between the two groups was statistically insignificant. Conclusion: A single-day postoperative dose of antibiotics effectively prevents postoperative wound infection following non-instrumented lumbar spinal surgery and is not associated with a higher infection rate.