Miracle-dz/UniFAR-FTUs huggingface dataset:
Postoperative Pain Control and Opioid Usage Patterns among Patients Undergoing Thyroidectomy and Parathyroidectomy

Objectives To examine opioid-prescribing patterns after endocrine surgery. To evaluate factors associated with postoperative pain and opioid use. Study Design Cross-sectional. Setting Academic university health system. Subjects and Methods The study sample included 209 patients who underwent total thyroidectomy, hemithyroidectomy, or parathyroidectomy by 4 surgeons between August 2015 and November 2017. Eighty-nine patients completed a phone survey about postoperative pain and opioid use. Prescription, demographic, and comorbidity data were collected retrospectively. Patient characteristics associated with opioid use, use of ≥10 opioid pills, and pain score were identified via chi-square, t test, analysis of variance, or Pearson correlation. Identified factors were further assessed with multivariable logistic and linear regression modeling. Results The median numbers of opioid pills prescribed were 20 for total thyroidectomy, 25 for hemithyroidectomy, and 20 for parathyroidectomy, and the median numbers of pills used were 1.5, 2, and 0, respectively. Of 1947 total prescribed pills, 19.7% were reported to be taken. The number of pills meeting the opioid needs of 80% of these patients was 10. In multivariable analyses, older age was associated with lower odds of opioid use (odds ratio, 0.97; 95% CI, 0.94-0.999; P = .04) and lower pain scores (Pearson correlation coefficient, –0.05; 95% CI, –0.10 to 0.001, P = .04). Charlson Comorbidity Index score >5 was associated with use of ≥10 pills (odds ratio, 6.62; 95% CI, 1.60-27.50; P = .01). Conclusion Excess opioids are often prescribed for endocrine surgery. By using an ideal pill number and understanding predictors of postoperative pain, surgeons can more adequately treat pain and limit excess opioid prescriptions.
Face Landmark-based Speaker-independent Audio-visual Speech Enhancement in Multi-talker Environments

In this paper, we address the problem of enhancing the speech of a speaker of interest in a cocktail party scenario when visual information of the speaker of interest is available.Contrary to most previous studies, we do not learn visual features on the typically small audio-visual datasets, but use an already available face landmark detector (trained on a separate image dataset). The landmarks are used by LSTM-based models to generate time-frequency masks which are applied to the acoustic mixed-speech spectrogram. Results show that: (i) land-mark motion features are very effective features for this task, (ii) similarly to previous work, reconstruction of the target speaker’s spectrogram mediated by masking is significantly more accurate than direct spectrogram reconstruction, and (iii) the best masks depend on both motion landmark features and the input mixed-speech spectrogram.To the best of our knowledge, our proposed models are the first models trained and evaluated on the limited size GRID and TCD-TIMIT datasets, that achieve speaker-independent speech enhancement in a multi-talker setting.
Anatomy Teaching, a “Model” Answer? Evaluating “Geoff”, a Painted Anatomical Horse, as a Tool for Enhancing Topographical Anatomy Learning

Development of new methods for anatomy teaching is increasingly important as we look to modernize and supplement traditional teaching methods. In this study, a life‐sized equine model, “Geoff,” was painted with surface and deep anatomical structures with the aim of improving students’ ability to convert theoretical knowledge into improved topographical anatomy knowledge on the live horse. Third and fourth year veterinary medicine students (n = 45) were randomly allocated into experimental (used “Geoff”) and control (used textbook) groups. The efficacy of the model was evaluated through a structured oral exam using a live horse. Questionnaires gathered information on student confidence and enjoyment of the task. There was no significant difference in the performance of experimental and control groups either immediately (44±20% vs. 40±21%; P = 0.504) or 9 weeks after the learning intervention (55±17% vs. 55±20%; P = 0.980). There were however specific questions on which the experimental group performed better than controls, and for which gender effects were apparent. The students using “Geoff” showed a transient gain in confidence following the session (Likert scale 2.7 to 3.6) however the initial increase was no longer present at the second test. There was a significant influence of gender on confidence with greater confidence gains in females in the Experimental group. The students found the model to be extremely useful and both groups found the sessions enjoyable. The model will be of benefit as a complementary learning tool for students.
ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data

We have fully integrated public chromatin chromatin immunoprecipitation sequencing (ChIP‐seq) and DNase‐seq data (n > 70,000) derived from six representative model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast), and have devised a data‐mining platform—designated ChIP‐Atlas (http://chip-atlas.org). ChIP‐Atlas is able to show alignment and peak‐call results for all public ChIP‐seq and DNase‐seq data archived in the NCBI Sequence Read Archive (SRA), which encompasses data derived from GEO, ArrayExpress, DDBJ, ENCODE, Roadmap Epigenomics, and the scientific literature. All peak‐call data are integrated to visualize multiple histone modifications and binding sites of transcriptional regulators (TRs) at given genomic loci. The integrated data can be further analyzed to show TR–gene and TR–TR interactions, as well as to examine enrichment of protein binding for given multiple genomic coordinates or gene names. ChIP‐Atlas is superior to other platforms in terms of data number and functionality for data mining across thousands of ChIP‐seq experiments, and it provides insight into gene regulatory networks and epigenetic mechanisms.
A Survey of Current Prophylactic Treatment for Ophthalmia Neonatorum in Croatia and a Review of International Preventive Practices

Background Ophthalmia neonatorum, or neonatal conjunctivitis, is an acute infection that occurs within the first 28 days of life. This aim of this survey was to evaluate the current methods of preventive treatment for ophthalmia neonatorum in maternity hospitals in Croatia. Material/Methods The annual hospital birth rate in Croatia is approximately 40,000. A clinical survey was undertaken with data collected using questionnaires sent to all 32 maternity hospitals in Croatia. There was a 100% response rate to the questionnaires. Results Preventive treatment for ophthalmia neonatorum was administrated to all newborns in 75% (24/32) of Croatian maternity hospitals. In 45.8% of maternity hospitals, (11/32) these procedures were performed within the first hour after birth. In 54.2% of maternity hospitals (13/32), preventive treatment for ophthalmia neonatorum was administrated to all newborns from one to three hours after birth. The main treatment agent was tobramycin (83.3%). Other topical prophylactic treatments included povidone-iodine (8.3%), erythromycin (4.2%), and silver nitrate (4.2%). In 25% of obstetric units, prophylaxis for ophthalmia neonatorum was not used routinely, but in cases of diagnosed neonatal conjunctivitis, antibiotic treatment with tobramycin was mainly used. Conclusions A survey of all 32 maternity hospitals in Croatia showed variation in the prevalence of preventive treatment for ophthalmia neonatorum and the methods used. These findings support the need to implement standardized preventive measures that both conform to international clinical guidelines and recognize treatment availability in Croatia, where topical povidone-iodine is currently preferred for the prevention of ophthalmia neonatorum.
Firearm Homicides and Suicides in Major Metropolitan Areas — United States, 2012–2013 and 2015–2016

Firearm homicides and suicides represent a continuing public health concern in the United States. During 2015-2016, a total of 27,394 firearm homicides (including 3,224 [12%] among persons aged 10-19 years) and 44,955 firearm suicides (including 2,118 [5%] among persons aged 10-19 years) occurred among U.S. residents (1). This report updates an earlier report (2) that provided statistics on firearm homicides and suicides in major metropolitan areas during 2006-2007 and 2009-2010, and places continued emphasis on youths, in recognition of the importance of early prevention efforts. Firearm homicide and suicide rates were determined for the 50 most populous U.S. metropolitan statistical areas (MSAs)* during 2012-2013 and 2015-2016 using mortality data from the National Vital Statistics System (NVSS) and population data from the U.S. Census Bureau. In contrast to the earlier report, which indicated that firearm homicide rates among persons of all ages had been declining both nationally and in large MSAs overall, current findings show that rates have returned to levels comparable to those observed during 2006-2007. Consistent with the earlier report, these findings show that firearm suicide rates among persons aged ≥10 years have continued to increase, both nationally and in large MSAs overall. Although firearm suicide rates among youths remain notably lower than those among persons of all ages, youth rates have also increased both nationally and in large MSAs collectively. These findings can inform ongoing development and monitoring of strategies directed at reducing firearm-related violence.
HIV-1 envelope glycan modifications that permit neutralization by germline-reverted VRC01-class broadly neutralizing antibodies

Broadly neutralizing antibody (bnAb) induction is a high priority for effective HIV-1 vaccination. VRC01-class bnAbs that target the CD4 binding site (CD4bs) of trimeric HIV-1 envelope (Env) glycoprotein spikes are particularly attractive to elicit because of their extraordinary breadth and potency of neutralization in vitro and their ability to protect against infection in animal models. Glycans bordering the CD4bs impede the binding of germline-reverted forms of VRC01-class bnAbs and therefore constitute a barrier to early events in initiating the correct antibody lineages. Deleting a subset of these glycans permits Env antigen binding but not virus neutralization, suggesting that additional barriers impede germline-reverted VRC01-class antibody binding to functional Env trimers. We investigated the requirements for functional Env trimer engagement of VRC01-class naïve B cell receptors by using virus neutralization and germline-reverted antibodies as surrogates for the interaction. Targeted deletion of a subset of N-glycans bordering the CD4bs, combined with Man5 enrichment of remaining N-linked glycans that are otherwise processed into larger complex-type glycans, rendered HIV-1 426c Env-pseudotyped virus (subtype C, transmitted/founder) highly susceptible to neutralization by near germline forms of VRC01-class bnAbs. Neither glycan modification alone rendered the virus susceptible to neutralization. The potency of neutralization in some cases rivaled the potency of mature VRC01 against wildtype viruses. Neutralization by the germline-reverted antibodies was abrogated by the known VRC01 resistance mutation, D279K. These findings improve our understanding of the restrictions imposed by glycans in eliciting VRC01-class bnAbs and enable a neutralization-based strategy to monitor vaccine-elicited early precursors of this class of bnAbs.
Optical Versus Virtual Microscope for Medical Education: A Systematic Review

Many technological innovations have changed the traditional practice of medical education and clinical practice. Whole slide imaging (WSI) technology provided an unique way of viewing conventional glass slides in histology and pathology laboratories. The WSI technology digitalized glass slide images and made them readily accessible via the Internet using tablets or computers. Users utilized the pan‐and‐zoom function to view digital images of slides, also referred to as the virtual microscope (VM), simulating use of an optical microscope (OM). Several articles have reported various outcomes on the utility of VM in teaching laboratories. Recently, the Royal College of Physicians and Surgeons of Canada certification examinations for anatomical pathologists ha completely adopted VM for the national licensing examination. To better inform medical educators, there is an urgent need for more structured reviews to draw evidence‐based conclusions on the effectiveness of VM and learner’s perceptions, in comparison to OM. The current study provides a descriptive summary of published outcomes using the systematic review approach. In conclusion, medical students’ performance was improved with adoption of VM into the curriculum and recognized as a preferred learning modality, compared to OM. On the contrary, resident learners’ performance was comparable between using OM and VM, with OM being the favored slide‐viewing modality.
In Patients We Trust: Reliability of Self-Reported Weight and Height in Nuclear Medicine Patients

The aim of the study was to assess the reliability of the self-reported weight and height of nuclear medicine patients in view of recommendations for weight-dependent tracer application for imaging and therapy. Methods: In total, 824 patients (334 men and 490 women) were asked to report their weight and height before imaging or therapy and their level of confidence. Subsequently, the weight and height of each patient were measured, and body mass index, body surface area, and lean body mass were calculated. Differences between reported and true values were compared for statistically significant differences. Results: The average patient age was 60 ± 14 y (range, 17–91 y). An over- or underestimation of weight by at least 10% was observed in 2% of patients, and height was overestimated by 1% by the patients. The BMI calculation was affected by incorrect self-reported values. Conclusion: Most self-reported weights and heights of nuclear medicine patients are accurate. However, since over- and underestimation of weight and height lead to incorrect body mass index, body surface area, and lean body mass values, patient weights should be measured at least for patients receiving a weight-adapted therapy or if quantification in PET/CT is needed.
Adoption of routine virologic testing and predictors of virologic failure among HIV-infected children on antiretroviral treatment in western Kenya

Background Access to routine virologic monitoring, critical to ensuring treatment success, remains limited in low- and middle-income countries. We report on implementation of routine viral load (VL) monitoring and risk factors for virologic failure among HIV-infected children on antiretroviral treatment (ART) in Western Kenya. Methods Routine VL testing was introduced in western Kenya in November 2013. We performed a case-control study among 1190 HIV-infected children ≤15 years on ART who underwent routine VL testing June 2014–May 2015. A random sample of 98 cases (virologic failure define as VL >1000 cps/mL) and 201 controls (VL <1000 cps/mL) from five facilities in three high HIV prevalence counties in Kenya were followed for a minimum of 12 months. Data from patient charts were analyzed using logistic regression to determine factors associated with failure to attain virologic suppression at initial routine and subsequent VL testing among cases. Results Overall, 1190 (94%) children with a median age of 8 years underwent routine VL testing of whom (37%) had virological failure. Among the 299 cases and controls, WHO stage, baseline CD4 count and time since ART initiation were not associated with virologic failure during the follow-up period. In multivariable analysis, unsuppressed children at initial test were more likely to be male (adjusted Odds Ratio (aOR) 2.1, 95% Confidence Interval (CI) 2.1–3.6) and have had an ART regimen change (aOR 2.0, CI 1.0–3.7) than controls. Of the two-thirds of children 201/299 who had a subsequent VL performed, VL suppression was greater among those suppressed at initial test 126/135 (93.3%) compared to children with virologic failure 15/66 (22.7%, p<0.0001). Among those failing at first test who achieved viral suppression in follow up, 12/15 (80%) were on a protease inhibitor (PI)-based regimen. In the multivariable analysis of children with subsequent VL testing, children on PI-based 2nd line regimens were 10-fold more likely to achieve viral suppression than children on first-line NNRTI-based ART (adjusted Odds Ratio [aOR] 0.1; 95%CI 0.0–0.4). Conclusion Coverage of initial routine viral load testing among children on ART in western Kenya is high. However, subsequent testing and virologic suppression are low in children with virologic failure on initial routine viral load test. There is an urgent need to improve management and viral load monitoring of children living with HIV experiencing treatment failure to ensure improved long-term outcomes.
Length of Hair Affects P1 and N170 Latencies for Perception of Women's Faces

This study investigated the relationship between length of hair in facial stimuli and latency and amplitude of the P1 and N170 components of event-related potentials during facial perception. Electroencephalography was recorded from 21 Japanese participants (four men, 17 women) who were shown pictures of faces with one of three lengths of hair: long, medium length, or short. In addition, we used both fixed-size and variable-size blocks. In fixed-size blocks, the three types of stimuli were matched to have the same overall size; in variable-size blocks, long hair stimuli were the biggest, medium length hair stimuli were medium sized, and short hair stimuli were the smallest. We analyzed P1 latency and amplitude using two-way (6 × 2) repeated-measures analysis of variance over length of hair and electrode; N170 latency and amplitude were analyzed using three-way (6 × 2 × 2) repeated-measures analysis of variance over length of hair, hemisphere, and electrode. The latency of P1 to faces with short hair in variable-size blocks was significantly longer than that to the other five stimulus types (p < .01 for four of the other types; p = .083 for medium length hair in variable-size blocks). The latency of N170 to faces with long hair in variable-size blocks was significantly shorter than that to faces with medium length hair and short hair in variable-size blocks (p = .026 and p = .086, respectively). These results indicate that length of hair influenced P1 and N170 latency, supporting the notion that length of hair is a significant external facial feature. Because long hair attracted participants' attention, there was early perceptual processing of this feature. In contrast, because short hair did not attract attention, perceptual processing of this feature was late.
Default Mode Network Lateralization and Memory in Healthy Aging and Alzheimer’s Disease

Lateralization of default mode network (DMN) functioning has been shown to change with age. Similarly, lateralization of frontal lobe function has been shown to decline in age. The impact of amyloid pathology and the progression of Alzheimer’s disease (AD) on resting state lateralization has not been investigated. Due to the preferential involvement of the left hemisphere in verbal tasks, there may be a benefit to higher levels of left-lateralization in the performance of verbal memory tasks. Here we compared functional lateralization of the anterior and posterior DMN between four groups of participants: amyloid negative (Aβ-) and amyloid positive (Aβ+) groups with normal cognition (NC), and Aβ+ groups with mild cognitive impairment (Aβ+MCI) or dementia (Aβ+AD). Differences were evident between groups in posterior DMN; the Aβ-NC group was more left-lateralized than both cognitively impaired Aβ+ groups. There was no difference in anterior DMN. No differences in overall network connectivity between groups were observed, suggesting that the functional lateralization finding is not secondary to general changes in connectivity. Left-lateralization of both networks was associated with better verbal recall performance. Older subjects, overall, had less left functional lateralization of the anterior DMN.
Numerical Processing and Executive Functioning in Early Versus Middle Childhood: A Japanese Sample

Many previous studies have investigated developmental differences in numerical processing by manipulating numerical distance and physical size in a number sequence. While it has been theorized that children's maturity level in executive functioning affects their numerical processing, the interaction between numerical processing and executive functioning through development remains unclear. We divided 60 Japanese school children, aged 8–12 years, into three age-related groups (second graders, fourth graders, and sixth graders) and had them perform physical and numerical comparison Stroop tasks. In the physical comparison task, the numerical Stroop effect (i.e., automatic numerical processing) was evident in each group, but, in the numerical comparison task, the numerical distance effect (i.e., intentional numerical processing) was evident in each group. Also, in the numerical comparison task, the size congruity effect (an index of the attentional and inhibitory control mechanisms of executive functioning) was more salient among second graders than among fourth or sixth graders. These results suggest that numerical processing matures and then plateaus just before primary school, while executive functioning continues to develop. Thus, these data provide evidence of a developmental dissociation between numerical processing and executive functioning.
SALaR: Scalable and Adaptive Designs for Large Message Reduction Collectives

Message Passing Interface (MPI), thus far, has remained a dominant programming model to program large-scale scientific applications. Collective communication operations in MPI are of significant importance due to their communication intensive nature and use in scientific applications. With the emergence of multi-/many-core systems and rise of deep learning applications, it is important to revisit MPI collectives, particularly MPI Allreduce to exploit vast parallelism offered by modern architectures. In this paper, we take up this challenge and propose Scalable and Adaptive designs for Large message Reduction collectives (SALaR). We focus on MPI Allreduce due to its use in deep learning frameworks and propose new designs that can significantly improve its performance by exploiting architectural features of modern multi-/many-cores in tandem with high-throughput network such as InfiniBand. We also propose a theoretical model to analyze communication and computation cost and use these insights to guide our designs. The evaluation of the proposed SALaR based designs shows significant performance gains over state-of-the-art designs on a wide variety of micro-benchmarks and applications.
From Drosophila segmentation to human cancer therapy

ABSTRACT First described in Drosophila, Hedgehog signalling is a key regulator of embryonic development and tissue homeostasis and its dysfunction underlies a variety of human congenital anomalies and diseases. Although now recognised as a major target for cancer therapy as well as a mediator of directed stem cell differentiation, the unveiling of the function and mechanisms of Hedgehog signalling was driven largely by an interest in basic developmental biology rather than clinical need. Here, I describe how curiosity about embryonic patterning led to the identification of the family of Hedgehog signalling proteins and the pathway that transduces their activity, and ultimately to the development of drugs that block this pathway. Summary: This Primer explores the fundamental impact of developmental biology on our understanding and therapeutic control of the hedgehog signalling pathway.