Miracle-dz/UniFAR-FTUs huggingface dataset:
Adjusting for social risk factors impacts performance and penalties in the hospital readmissions reduction program

OBJECTIVE Medicare's Hospital Readmissions Reduction Program (HRRP) does not account for social risk factors in risk adjustment, and this may lead the program to unfairly penalize safety-net hospitals. Our objective was to determine the impact of adjusting for social risk factors on HRRP penalties. STUDY DESIGN Retrospective cohort study. DATA SOURCES/STUDY SETTING Claims data for 2 952 605 fee-for-service Medicare beneficiaries with acute myocardial infarction (AMI), congestive heart failure (CHF) or pneumonia from December 2012 to November 2015. PRINCIPAL FINDINGS Poverty, disability, housing instability, residence in a disadvantaged neighborhood, and hospital population from a disadvantaged neighborhood were associated with higher readmission rates. Under current program specifications, safety-net hospitals had higher readmission ratios (AMI, 1.020 vs 0.986 for the most affluent hospitals; pneumonia, 1.031 vs 0.984; and CHF, 1.037 vs 0.977). Adding social factors to risk adjustment cut these differences in half. Over half the safety-net hospitals saw their penalty decline; 4-7.5 percent went from having a penalty to having no penalty. These changes translated into a $17 million reduction in penalties to safety-net hospitals. CONCLUSIONS Accounting for social risk can have a major financial impact on safety-net hospitals. Adjustment for these factors could reduce negative unintended consequences of the HRRP.
Quality of life of diabetes amputees following major and minor lower limb amputations.

INTRODUCTION Minor amputation was performed as a salvage procedure because most of the patients were not able to ambulate and become dependent following major amputation. Minor amputation is defined as amputation at the level of ankle joint and below while major amputation is defines by amputation above the ankle joint. The aim of this study was to compare the quality of life among diabetes patients following major and minor amputations. METHODS A total of 94 diabetes patients were reviewed six months following amputation. Their walking ability, dependency status and quality of life were evaluated, using the Malay translated version of the Short Form Health Survey 36 (SF-36) questionnaire. RESULTS During the follow up only three patients (8.3%) following major amputation were dependant compared to 30 patients (51.7%) following minor amputation. Forty-nine (84.5%) of minor amputation and only 15 (41.7%) of major amputation patients were ambulating independently. Patients with minor amputation have significantly better Physical functioning, Role - physical, General health, Role - emotional, and Mental health score (p<0.001). However, they have worse BP and SF score than those following major amputation (p<0.001). The VT score of both groups were not significantly different. CONCLUSION Patients with minor amputation are more independent, ambulatory and had better quality of life than those with major amputation. Despite the risk of persistent infection and amputation stump complication, minor amputation should be attempted in diabetes patients.
Phylogenomic Analyses of Bradyrhizobium Reveal Uneven Distribution of the Lateral and Subpolar Flagellar Systems, Which Extends to Rhizobiales

Dual flagellar systems have been described in several bacterial genera, but the extent of their prevalence has not been fully explored. Bradyrhizobium diazoefficiens USDA 110T possesses two flagellar systems, the subpolar and the lateral flagella. The lateral flagellum of Bradyrhizobium displays no obvious role, since its performance is explained by cooperation with the subpolar flagellum. In contrast, the lateral flagellum is the only type of flagella present in the related Rhizobiaceae family. In this work, we have analyzed the phylogeny of the Bradyrhizobium genus by means of Genome-to-Genome Blast Distance Phylogeny (GBDP) and Average Nucleotide Identity (ANI) comparisons of 128 genomes and divided it into 13 phylogenomic groups. While all the Bradyrhizobium genomes encode the subpolar flagellum, none of them encodes only the lateral flagellum. The simultaneous presence of both flagella is exclusive of the B. japonicum phylogenomic group. Additionally, 292 Rhizobiales order genomes were analyzed and both flagellar systems are present together in only nine genera. Phylogenetic analysis of 150 representative Rhizobiales genomes revealed an uneven distribution of these flagellar systems. While genomes within and close to the Rhizobiaceae family only possess the lateral flagellum, the subpolar flagellum is exclusive of more early-diverging families, where certain genera also present both flagella.
Phytotoxicity of a Culture Filtrate Produced by Stemphylium solani of Cotton.

Stemphylium solani, which causes a new leaf blight of cotton, was suspected of producing a phytotoxin. Studies were conducted to examine the relationship between the reaction of different cotton cultivars and of some unrelated host species to the pathogen and its toxin-containing culture filtrates. Seven single spore isolates of S. solani from cotton and their toxin-containing culture filtrates were used for leaf and root bioassays. An isolate of S. solani from tomato was also used for comparison. The phytotoxic effect was isolate dependent. Culture filtrates of five isolates killed 40 to 60% of the cotton seedlings when incubated for 4 days at 10-1 dilution. At 10-2 dilution, the culture filtrates of most of the isolates affected the development of the root system but failed to kill any seedling. The phytotoxic effect of the culture filtrate was not degraded by autoclaving. A high correlation coefficient between the percentage of the leaf area infected (LAI) by S. solani and the percentage of the necrotic leaf area (LAN) by the culture filtrate was observed when one of the aggressive isolates and its culture filtrate were tested against adult plants of 38 cotton cultivars (r = 0.86). Cultivars CNPA T-1180-23, CNPA-PRECOCE 2, PR 94-215, and PR 94-82 demonstrated resistance to the pathogen as well as insensitivity or moderate sensitivity to its toxin. Cultivars showing intermediate reaction to the pathogen also showed intermediate reaction to its culture filtrate. Similarly, the highly susceptible cultivars Paraná 3, PR 93-129, and PR 94-216 also were highly sensitive to the culture filtrate. Of the 18 plant species belonging to 18 genera, eight were susceptible to the pathogen. With two exceptions, susceptible hosts were also sensitive to the culture filtrate, whereas nonsusceptible hosts were insensitive. A component of the culture filtrate was regarded as a pathogenicity factor.
Biopsy of diffuse intrinsic pontine gliomas?

The authors have performed an important study in which 7 patients with diffuse intrinsic pontine gliomas (DIPGs) underwent biopsy at their institution. These cases were selected from a total of 54 involving patients with pontine tumors who presented to their institution since 2004. The cases in which biopsy was performed were deemed “atypical” in terms of neuroimaging findings. Of these, 2 were shown by neuropathological examination and hierarchical cluster analysis to be cases of pontine primitive neuroectodermal tumors (PNETs), which were treated in a different manner from DIPGs—with aggressive chemotherapy and tandem autologous stem cell transplant in conjunction with radiation therapy. In 2006, Zagzag et al.2 reported on 7 cases of brainstem tumors that were proven to be PNETs on the basis of biopsy. In their series, the brainstem PNETs occurred in younger children and were primarily focal lesions in contrast to the DIPGs. However, this report raised the specter that not all intrinsic brainstem lesions in children are DIPGs, and that biopsy in select circumstances would be warranted. In the current report, Sufit et al.1 have used the Affymetrix U133 Plus 2.0 GeneChip microarray to examine the 7 brainstem cases in which biopsy specimens were obtained, and have compared these results against those for other pediatric brain tumors, including medulloblastoma, atypical teratoid/rhabdoid tumor, ependymoma, and ganglioglioma to name a few. Their cluster analysis shows that pontine PNETs have a similar genetic profile to supratentorial PNETs, but a different profile, for the most part, from DIPGs. It should be noted that some of the histologically confirmed DIPGs clustered closely to the pontine PNETs. Why is this study important? It is important because we are approaching an era in which molecular studies of biopsy specimens from brain tumors can be used to help select or validate the use of subsequent therapies, as was shown in the 2 cases of pontine PNETs in which biopsy was performed here. The issue of whether biopsy specimens should be obtained in pontine lesions with atypical DPIG neuroimaging characteristics is becoming less controversial. At our institution, children with pontine tumors undergo biopsy if they have atypical neuroimaging or clinical features. It would be reasonable to perform biopsies of typical DIPGs within the context of a welldefined and structured clinical trial in which molecular analyses are being performed to advance our working knowledge of the genetic origins of these tumors. Biopsy can be performed, as demonstrated in this case series, with acceptable morbidity. Future studies of brainstem biopsies may take advantage of the latest Affymetrix Gene 1.1 ST array, which “tiles” across the entire transcript, as opposed to the U133 Plus 2.0 GeneChip array, in which the probes were designed to hybridize to the 3′ end of the transcript. These newly designed gene arrays may provide a more robust characterization of the genetic profile of brainstem tumors in children. (http://thejns.org/doi/abs/10.3171/2012.2.PEDS1237)
HDAC1 Is a Required Cofactor of CBFβ-SMMHC and a Potential Therapeutic Target in Inversion 16 Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a neoplastic disease characterized by the uncontrolled proliferation and accumulation of immature myeloid cells. A common mutation in AML is the inversion of chromosome 16 [inv (16)], which generates a fusion between the genes for core binding factor beta (CBFB) and smooth muscle myosin heavy chain gene (MYH11), forming the oncogene CBFB-MYH11. The expressed protein, CBFβ-SMMHC, forms a heterodimer with the key hematopoietic transcription factor RUNX1. Although CBFβ-SMMHC was previously thought to dominantly repress RUNX1, recent work suggests that CBFβ-SMMHC functions together with RUNX1 to activate transcription of specific target genes. However, the mechanism of this activity or a requirement for additional cofactors is not known. Here, we show that the epigenetic regulator histone deacetylase 1 (HDAC1) forms a complex with CBFβ-SMMHC, colocalizes with RUNX1 and CBFβ-SMMHC on the promoters of known fusion protein target genes, and that Hdac1 is required for expression of these genes. These results imply that HDAC1 is an important component of the CBFβ-SMMHC transcriptional complex, and that leukemia cells expressing the fusion protein may be sensitive to treatment with HDAC1 inhibitors. Using a knock-in mouse model expressing CBFβ-SMMHC, we found that in vivo treatment with the HDAC1 inhibitor entinostat decreased leukemic burden, and induced differentiation and apoptosis of leukemia cells. Together, these results demonstrate that HDAC1 is an important cofactor of CBFβ-SMMHC and a potential therapeutic target in inv (16) AML. Implications: This report describes a novel role for HDAC1 as a cofactor for the leukemogenic fusion protein CBFβ-SMMHC and shows that inhibitors of HDAC1 effectively target leukemia cells expressing the fusion protein in vivo.
Small RNA-Seq Analysis Reveals miRNA Expression Dynamics Across Tissues in the Malaria Vector, Anopheles gambiae

Malaria continues to be a major global health problem, where disease transmission is deeply linked to the repeated blood feeding nature of the anautogenous mosquito. Given the tight link between blood feeding and disease transmission, understanding basic biology behind mosquito physiology is a requirement for developing effective vector-borne disease control strategies. In the mosquito, numerous loss of function studies with notable phenotypes demonstrate microRNAs (miRNAs) play significant roles in mosquito physiology. While the field appreciates the importance of a handful of miRNAs, we still need global mosquito tissue miRNA transcriptome studies. To address this need, our goal was to determine the miRNA transcriptome for multiple tissues of the pre-vitellogenic mosquito. To this end, by using small RNA-Seq analysis, we determined miRNA transcriptomes in tissues critical for mosquito reproduction and immunity including (i) fat body-abdominal wall enriched tissues, (ii) midguts, (iii) ovaries, and (iv) remaining tissues comprised of the head and thorax. We found numerous examples of miRNAs exhibiting pan-tissue high- or low- expression, tissue exclusion, and tissue enrichment. We also updated and consolidated the miRNA catalog and provided a detailed genome architecture map for the malaria vector, Anopheles gambiae. This study aims to build a foundation for future research on how miRNAs and potentially other small RNAs regulate mosquito physiology as it relates to vector-borne disease transmission.
Betaine ameliorates prenatal valproic‐acid‐induced autism‐like behavioral abnormalities in mice by promoting homocysteine metabolism

Abnormally high levels of homocysteine (Hcy) are associated with autism spectrum disorder. Betaine is a methyl group donor in Hcy metabolism, and is known to prevent noxious Hcy accumulation. This study explored whether betaine could influence Hcy metabolism in a mouse model of autism and ameliorate behavioral abnormalities.
Homocysteine and small vessel stroke: A mendelian randomization analysis

Trials of B vitamin therapy to lower blood total homocysteine (tHcy) levels for prevention of stroke are inconclusive. Secondary analyses of trial data and epidemiological studies suggest that tHcy levels may be particularly associated with small vessel stroke (SVS). We assessed whether circulating tHcy and B vitamin levels are selectively associated with SVS, but not other stroke subtypes, using Mendelian randomization.
Neuronal Adaptation Reveals a Suboptimal Decoding of Orientation Tuned Populations in the Mouse Visual Cortex

Sensory information is encoded by populations of cortical neurons. Yet, it is unknown how this information is used for even simple perceptual choices such as discriminating orientation. To determine the computation underlying this perceptual choice, we took advantage of the robust visual adaptation in mouse primary visual cortex (V1). We first designed a stimulus paradigm in which we could vary the degree of neuronal adaptation measured in V1 during an orientation discrimination task. We then determined how adaptation affects task performance for mice of both sexes and tested which neuronal computations are most consistent with the behavioral results given the adapted population responses in V1. Despite increasing the reliability of the population representation of orientation among neurons, and improving the ability of a variety of optimal decoders to discriminate target from distractor orientations, adaptation increases animals' behavioral thresholds. Decoding the animals' choice from neuronal activity revealed that this unexpected effect on behavior could be explained by an overreliance of the perceptual choice circuit on target preferring neurons and a failure to appropriately discount the activity of neurons that prefer the distractor. Consistent with this all-positive computation, we find that animals' task performance is susceptible to subtle perturbations of distractor orientation and optogenetic suppression of neuronal activity in V1. This suggests that to solve this task the circuit has adopted a suboptimal and task-specific computation that discards important task-related information. SIGNIFICANCE STATEMENT A major goal in systems neuroscience is to understand how sensory signals are used to guide behavior. This requires determining what information in sensory cortical areas is used, and how it is combined, by downstream perceptual choice circuits. Here we demonstrate that when performing a go/no-go orientation discrimination task, mice suboptimally integrate signals from orientation tuned visual cortical neurons. While they appropriately positively weight target-preferring neurons, they fail to negatively weight distractor-preferring neurons. We propose that this all-positive computation may be adopted because of its simple learning rules and faster processing, and may be a common approach to perceptual decision-making when task conditions allow.
Comparison of Academic Performance in Traditional and Flipped Classrooms and Students' Attitudes of the Flipped Experience.

The flipped classroom method allows students to learn formative material before class while acquiring higher-order learning in-class. The purpose of this study was to compare learning outcomes between traditional lecture and the flipped classroom model in a Doctor of Physical Therapy program and to assess student satisfaction with the flipped classroom method. METHODS Three cohorts of first-year students, Classes 2015, 2016, and 2017 (Class A, B, C respectively) from a 3-year physical therapy education program. Classes were taught by traditional lectures for 1 year (Class A) and with the flipped model the next 2 years (Class B and C). Correlation analysis of examination questions between the cohorts was performed, with a = 0.05. A post-course survey evaluated the experience. RESULTS Correlation analysis of examination questions revealed high correlation with similar performance in all classes: Class A and B, r = 0.62; Class A and C, r = 0.57; Class B and C, r = 0.74. Students in both Class B and C felt the flipped experience met the learning objectives. CONCLUSIONS Learning outcomes of traditional lecture and flipped method classes were similar in our study. Student satisfaction with the flipped method may be related to student intrinsic motivation to complete the pre-class work.
Time-lapse imaging: the state of the art†

Abstract The introduction of time-lapse imaging to clinical in vitro fertilization practice enabled the undisturbed monitoring of embryos throughout the entire culture period. Initially, the main objective was to achieve a better embryo development. However, this technology also provided an insight into the novel concept of morphokinetics, parameters regarding embryo cell dynamics. The vast amount of data obtained defined the optimal ranges in the cell-cycle lengths at different stages of embryo development. This added valuable information to embryo assessment prior to transfer. Kinetic markers became part of embryo evaluation strategies with the potential to increase the chances of clinical success. However, none of them has been established as an international standard. The present work aims at describing new approaches into time-lapse: progress to date, challenges, and possible future directions. Summary Sentence Time-lapse imaging has considerably increased the amount of reliable and detailed information regarding embyo development, contributing to improve the embryo selection.
Impacts of thermal mismatches on chytrid fungus Batrachochytrium dendrobatidis prevalence are moderated by life stage, body size, elevation and latitude

Global climate change is increasing the frequency of unpredictable weather conditions; however, it remains unclear how species-level and geographic factors, including body size and latitude, moderate impacts of unusually warm or cool temperatures on disease. Because larger hosts and lower-latitude hosts generally have slower acclimation times, we hypothesized that their disease susceptibility increases under “thermal mismatches”, or differences between baseline climate and the temperature during surveying. Here, we examined how thermal mismatches interact with body size, life stage, habitat, latitude, elevation, phylogeny, and IUCN conservation status to predict infection prevalence of the chytrid fungus Batrachochytrium dendrobatidis (Bd) in a global analysis of 38,967 amphibian hosts. As hypothesized, we found that the susceptibility of larger hosts and hosts from lower latitudes was strongly influenced by thermal mismatches. Furthermore, hosts of conservation concern are more susceptible than others following thermal mismatches, suggesting that thermal mismatches might have contributed to recent amphibian declines. Data Accessibility Statement Should the manuscript be accepted, the data supporting the results will be archived in an appropriate public repository such as Dryad or Figshare and the data DOI will be included at the end of the article.
The Association of the Exposure to Work-Related Traumatic Events and Work Limitations among Firefighters: A Cross-Sectional Study

Many firefighters suffering from traumatic events while on duty participate in the work force. However, the impact of work-related traumatic events on work performance is unclear. To address this issue, we administered a work-related traumatic event experience survey, the health-related work limitations questionnaire, the Korea Depression Scale, and the World Health Organization quality of life assessment to firefighters from four cities in Korea. The health-related work limitations questionnaire measured limitations in their ability to perform three specific work demands—physical, psychosocial, and environmental. Of 685 firefighters enrolled in the study, 618 (90.2%) were included in the final analyses. Their mean age ± standard deviation (SD) was 41.1 ± 8.0 years and mean employment period ± SD was 163.0 ± 101.2 months. A large percentage of participants reported they had experienced work-related traumatic events. Among the firefighters, the total work limitation prevalence was 21.5%, 16.8% of them were limited in their abilities to perform physical work demands, 15.5% were limited in performing psychosocial work demands, and 13.8% were limited in their abilities to function without difficulty within the ambient work environment. Based on multivariable logistic regression, with having work-related traumatic event experience of a threat or injury to self, the odds ratio (OR) of having work limitations in physical (OR = 3.32, 95% CI = 1.17–9.41), psychosocial (OR = 3.05, 95% CI = 1.08–8.61), environmental (OR = 4.89, 95% CI = 1.66–14.40) work demands, and total work limitation (OR = 3.73, 95% CI = 1.44–9.68) increased significantly. With experiences of treating fatalities or injured patients, the OR of total work limitation increased significantly (OR = 2.07, 95% CI = 1.09–3.91). We demonstrated a relationship between the firefighters’ exposure to work-related traumatic events and their work limitations. A professional care management system for firefighters to prevent and manage work-related traumatic events should be developed in order to protect and improve their performance ability.