Miracle-dz/UniFAR-FTUs huggingface dataset:
Gender inequalities among authors who contributed equally

We analyzed 2898 scientific papers published between 1995 and 2017 in which two or more authors shared the first author position. For papers in which the first and second authors made equal contributions, mixed-gender combinations were most frequent, followed by male-male and then female-female author combinations. For mixed-gender combinations, more male authors were in the first position, although the disparity decreased over time. For papers in which three or more authors made equal contributions, there were more male authors than female authors in the first position and more all-male than all-female author combinations. The gender inequalities observed among authors who made equal contributions are not consistent with random or alphabetical ordering of authors. These results raise concerns about female authors not receiving proper credit for publications and suggest a need for journals to request clarity on the method used to decide author order among those who contributed equally.
fNIRS Assessment during an Emotional Stroop Task among Patients with Depression: Replication and Extension

Objective Accumulated evidence collected via functional near-infrared spectroscopy (fNIRS) has been reported with regard to mental disorders. A previous finding revealed that emotional words evoke left frontal cortex activity in patients with depression. The primary aim of the current study was to replicate this finding using an independent dataset and evaluate the brain region associated with the severity of depression using an emotional Stroop task. Methods Oxygenized and deoxygenized hemoglobin recording in the brain by fNIRS on 14 MDD patients and 20 normal controls. Results Hyperactivated oxygenized hemoglobin was observed in the left frontal cortex on exposure to unfavorable stimuli, but no significant difference was found among patients with depression compared with healthy controls on exposure to favorable stimuli. This result is consistent with previous findings. Moreover, an evoked wave associated with the left upper frontal cortex on favorable stimuli was inversely correlated with the severity of depression. Conclusion Our current work using fNIRS provides a potential clue regarding the location of depression symptom severity in the left upper frontal cortex. Future studies should verify our findings and expand them into a precise etiology of depression.
Machine Learning and Integrative Analysis of Biomedical Big Data

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues.
The Cutaneous Inflammatory Response to Thermal Burn Injury in a Murine Model

Many burn interventions aim to target the inflammatory response as a means of enhancing healing or limiting hypertrophic scarring. Murine models of human burns have been developed, but the inflammatory response to injury in these models has not been well defined. The aim of this study was to profile inflammatory cell populations and gene expression relative to healing and scarring in a murine model of thermal burns. Cutaneous injuries were created on the dorsal region of C57Bl/6 mice using a heated metal rod. Animals were euthanized at selected time points over ten weeks, with the lesions evaluated using macroscopic measurements, histology, immunofluorescent histochemistry and quantitative PCR. The burn method generated a reproducible, partial-thickness injury that healed within two weeks through both contraction and re-epithelialization, in a manner similar to human burns. The injury caused an immediate increase in pro-inflammatory cytokine and chemokine expression, coinciding with an influx of neutrophils, and the disappearance of Langerhans cells and mast cells. This preceded an influx of dendritic cells and macrophages, a quarter of which displayed an inflammatory (M1) phenotype, with both populations peaking at closure. As with human burns, the residual scar increased in size, epidermal and dermal thickness, and mast cell numbers over 10 weeks, but abnormal collagen I-collagen III ratios, fibre organization and macrophage populations resolved 3–4 weeks after closure. Characterisation of the inflammatory response in this promising murine burn model will assist future studies of burn complications and aid in the preclinical testing of new anti-inflammatory and anti-scarring therapies.
Temporal and geospatial trends of adolescent intentional overdoses with suspected suicidal intent reported to a state poison control center

Abstract Background: In the United States, adolescent suicide attempts are increasing. Indiana has the highest rate of adolescent suicidal ideation in the US. Using the National Poison Data System (NPDS), we analyzed Indiana’s increase in suicide attempts by poisoning. Methods: Utilizing NPDS and Toxicall data repositories, we selected 10–19 year-old intentional overdose cases with suspected suicidal intent from 2006–2016. Age, sex, outcome, involved substances and case volume by weekday and month were assessed. Geospatial analysis of the proportion of cases by county was also performed. To determine the association between known social determinants of health and adolescent intentional overdose cases with suspected suicidal intent, we correlated county-wide statistics from the County Health Rankings and Roadmaps dataset from 2010–2016 with the proportion of teen suicide cases by county. Results: Over the eleven years, adolescent intentional overdoses with suspected suicidal intent cases significantly increased starting in 2012 (p-value < .001). The majority of cases (73.7%) involved females with an average age of 15.96 ± 0.27 years. Monday and Tuesday had the highest rates and Saturday had the lowest. June and July had the lowest case rate while November had the highest. The most commonly involved agents were over-the-counter analgesics and antidepressants. Geospatial analysis shows an increased number of cases in the northern third of the State. Among county statistics analyzed, only violent crime was associated, albeit intermittently, with the 11-year proportion of adolescent intentional overdoses with suspected suicidal intent by county. Conclusions: Intentional overdoses with suspected suicidal intent involving adolescent females are significantly increasing. These rates correlate with the school schedule with summer months and weekends having a lower frequency of calls. We did not find associations between county wide social determinants of care with the exception of violent crime. Further studies are needed to establish the factors that might better predict adolescents at risk for suicide.
Impact of educational attainment on the association between social class at birth and multimorbidity in middle age in the Aberdeen Children of the 1950s cohort study

Objective Multimorbidity (the coexistence of two or more health conditions) is increasingly prevalent. No long-term cohort study has examined the impact of contemporaneously measured birth social class along with educational attainment on adult self-reported multimorbidity. We investigated the impact of educational attainment on the relationship between social class at birth and adult self-reported multimorbidity in the Aberdeen Children of the 1950s (ACONF) cohort. Methods A prospective cohort study using the ACONF cohort. ACONF included 12 150 individuals born in Aberdeen, Scotland 1950–1956. In 2001, 7184 (64%) responded to a questionnaire providing information including self-reported morbidity and educational attainment. The exposure was father’s social class at birth from birth records and the outcome was self-reported multimorbidity. Logistic regression assessed the association between social class and multimorbidity with adjustment for gender, then by educational attainment and finally by childhood cognition and secondary school type. ORs and 95% CIs were presented. Results Of 7184 individuals (mean age 48, 52% female), 5.4% reported multimorbidity. Birth social class was associated with adult multimorbidity. For example, the OR of multimorbidity adjusted by gender was 0.62 (95% CI 0.39 to 1.00) in the highest social class group (I/II) in relation to the reference group (III (manual)) and was 1.85 (95% CI 1.19 to 2.88) in the lowest social class group. This was partially attenuated in all social class categories by educational attainment, for example, the OR was 0.74 (95% CI 0.45 to 1.21) in group I/II following adjustment. Conclusion Lower social class at birth was associated with developing multimorbidity in middle age. This was partially mediated by educational attainment and future research should consider identifying the other explanatory variables. The results are relevant to researchers and to those aiming to reduce the impact of multimorbidity.
Draft Genome Sequence of Hyperthermophilic, Halotolerant Parageobacillus toebii PW12, Isolated from the Tattapani Hot Spring, Northwest Himalayas

Here, we report the genome sequence of hyperthermophilic and halophilic Parageobacillus toebii PW12, isolated from the Tattapani hot spring in the northwest Himalayas. The genome size of Parageobacillus toebii PW12 is 3,210,377 bp. ABSTRACT Here, we report the genome sequence of hyperthermophilic and halophilic Parageobacillus toebii PW12, isolated from the Tattapani hot spring in the northwest Himalayas. The genome size of Parageobacillus toebii PW12 is 3,210,377 bp. The G+C content is 42.05%, and 3,382 coding sequences (CDS), 80 tRNAs, 5 noncoding RNAs (ncRNAs), and 4 CRISPR arrays were predicted.
Whole-Genome Sequencing of Legionella jordanis Strains NML 060502 and NML 130005, Recovered from a Lower Respiratory Tract Infection and Water, Respectively

Draft genome sequences of two strains of the rarely isolated organism Legionella jordanis, NML 060502 (from a patient with a lower respiratory infection) and NML 130005 (from water), were assembled and studied. Respectively, the genome sizes obtained were 2,927,328 bp and 3,101,130 bp, with G+C contents of 41.9% and 41.7%. ABSTRACT Draft genome sequences of two strains of the rarely isolated organism Legionella jordanis, NML 060502 (from a patient with a lower respiratory infection) and NML 130005 (from water), were assembled and studied. Respectively, the genome sizes obtained were 2,927,328 bp and 3,101,130 bp, with G+C contents of 41.9% and 41.7%.
Genome Sequence of Morganella morganii DG56-16, Isolated from Shinisaurus crocodilurus

The complete genome sequence of Morganella morganii DG56-16 was sequenced. This strain was isolated from the liver of a dead crocodile lizard (Shinisaurus crocodilurus). ABSTRACT The complete genome sequence of Morganella morganii DG56-16 was sequenced. This strain was isolated from the liver of a dead crocodile lizard (Shinisaurus crocodilurus). The genome size was 3.9 Mb, with a G+C content of 50.9%.
Complete Genome Sequence of an Influenza D Virus Strain Identified in a Pig with Subclinical Infection in the United States

Influenza D virus was first described in 2011 from a pig with respiratory disease; however, recent evidence indicates that cattle are the major viral reservoir. Here, we describe the genome sequence of the eighth complete swine-origin influenza D virus deposited into GenBank, D/swine/Kentucky/17TOSU1262/2017, which was collected at a 2017 swine exhibition. ABSTRACT Influenza D virus was first described in 2011 from a pig with respiratory disease; however, recent evidence indicates that cattle are the major viral reservoir. Here, we describe the genome sequence of the eighth complete swine-origin influenza D virus deposited into GenBank, D/swine/Kentucky/17TOSU1262/2017, which was collected at a 2017 swine exhibition.
Complete Genome Sequence of the Putative Phosphonate Producer Streptomyces sp. Strain I6, Isolated from Indonesian Mangrove Sediment

Streptomyces sp. strain I6 is a novel strain isolated from an Indonesian mangrove sediment sample. Bioinformatic analysis of the genome sequence of Streptomyces sp. I6 revealed 23 biosynthetic gene clusters. ABSTRACT Streptomyces sp. strain I6 is a novel strain isolated from an Indonesian mangrove sediment sample. Bioinformatic analysis of the genome sequence of Streptomyces sp. I6 revealed 23 biosynthetic gene clusters. One of them encodes the synthesis of a putative phosphonate secondary metabolite, a class of underexplored natural compounds with great pharmaceutical potential.
Physical Activity Pattern and Its Association with Glycaemic and Blood Pressure Control among People Living with Diabetes (PLWD) In The Ho Municipality, Ghana

Background Physical activity (PA) offers considerable health benefits for diabetic patients. However, extensive high levels of inactivity has been reported among diabetic patients. This study sought to assess the patterns of physical activity and its relationship with two management-relevant outcomes (glycaemic and blood pressure control)among people living with diabetes in the Ho Municipality, Ghana. Methods A hospital-based cross-sectional study was carried out from January 2017 to April 2017 among 150 purposively recruited diabetic patients who were receiving care at the diabetes clinics of the Volta Regional Hospital and the Ho Municipal Hospital. A semi-structured questionnaire was used in capturing socio-demographic information. Physical activity was assessed using the International Physical Activity Questionnaire Short Form. Glycaemic and blood pressure control were evaluated within a three-month period from patients' records. Results Physical activity estimates among participants were 21.33%, 48% and 30.67% for high, moderate and low PA respectively. Glycaemic control among the study participants was 33.33% and blood pressure control was 58.67%. Both glycaemic and blood pressure control were significantly associated with PA. Conclusion In this group of PLWD in the Ho Municipality, high levels of inactivity, uncontrolled glycaemia and blood pressure exist. However, glycaemic and blood pressure control may be modulated by moderate-intensity physical activity.
Sleeping mattress determinants and evaluation: a biomechanical review and critique

Background Sleeping mattress parameters significantly influence sleeping comfort and health, as reflected by the extensive investigations of sleeping support biomechanics to prevent sleep-related musculoskeletal problems. Methodology Herein, we review the current trends, research methodologies, and determinants of mattress biomechanics research, summarizing evidence published since 2008. In particular, we scrutinize 18 articles dealing with the development of new designs, recommendation criteria, instruments/methods of spine alignment evaluation, and comparative evaluation of different designs. Results The review demonstrated that mattress designs have strived for customization, regional features, and real-time active control to adapt to the biomechanical features of different body builds and postures. However, the suggested threshold or target values for desirable spine alignment and body pressure distribution during sleep cannot yet be justified in view of the lack of sufficient evidence. Conclusions It is necessary to formulate standard objectives and protocols for carrying out mattress evaluation.
Severe Pneumonia Caused by Coinfection With Influenza Virus Followed by Methicillin-Resistant Staphylococcus aureus Induces Higher Mortality in Mice

Background: Coinfection with influenza virus and bacteria is a major cause of high mortality during flu pandemics. Understanding the mechanisms behind such coinfections is of utmost importance both for the clinical treatment of influenza and the prevention and control of epidemics. Methods: To investigate the cause of high mortality during flu pandemics, we performed coinfection experiments with H1N1 influenza virus and Staphylococcus aureus in which mice were infected with bacteria at time points ranging from 0 to 7 days after infection with influenza virus. Results: The mortality rates of mice infected with bacteria were highest 0–3 days after infection with influenza virus; lung tissues extracted from these co-infected mice showed higher infiltrating cells and thicker lung parenchyma than lung samples from coinfected mice in which influenza virus was introduced at other times and sequences. The levels of interferon (IFN)-γ, tumor necrosis factor (TNF)-α, interleukin (IL)-8, and IL-6 in the 0–3 day coinfected group were significantly higher than those in the other groups (p < 0.01), as were the mRNA levels of IFN-γ, IL-6, and TNF-α. Coinfection with influenza virus and S. aureus led to high mortality rates that are directly dependent on the sequence and timing of infection by both pathogens. Moreover, coinfection following this particular schedule induced severe pneumonia, leading to increased mortality. Conclusions: Our data suggest that prevention of bacterial co-infection in the early stage of influenza virus infection is critical to reducing the risk of clinical mortality.
Expression and Function of Neuron-Glia-Related Cell Adhesion Molecule (NrCAM) in the Amygdalar Pathway

Neuron-Glia related cell adhesion molecule (NrCAM) is a candidate autism risk factor that promotes axon guidance through cytoskeletal linkages in developing brain but its role in limbic circuitry has not been investigated. In situ hybridization (ISH) and immunofluorescence staining showed that NrCAM is expressed in the developing amygdalar pathway of mouse embryos during outgrowth of projections in the stria terminalis, a major limbic tract that interconnects the central amygdala (CeA) with key targets in the bed nucleus of the stria terminalis (BNST). Analysis of fiber tracts in NrCAM mutant mice by Neurofilament protein immunohistochemistry showed pronounced defasciculation and misprojection of fibers in the ST. The defasciculation phenotype may result from impairment in NrCAM homophilic inter-axonal adhesion or axon repulsion from the secreted ligand Semaphorin 3F, which is expressed in limbic areas in proximity to the ST. Behavioral testing indicated that NrCAM null mice were impaired in context-dependent fear conditioning, in accord with altered amygdala-BNST connectivity, but displayed normal cued (tone-shock) conditioning. Results are consistent with the novel finding that NrCAM mediates fasciculation of axon fibers in the ST important for proper amygdalar-BNST circuitry and response to contextual fear conditioning.
Shared Knowledge and Verbal Communication in Football: Changes in Team Cognition Through Collective Training

One of the psychological mechanisms that contribute to effective and efficient team actions is team cognition, defined either as shared knowledge states about game situations, teammates’ skills, and action probabilities or direct communication processes in the team action itself. Particularly in interactive team sports (e.g., football), characterized by highly complex, dynamic, and uncertain situations, sharing a common understanding concerning potential future actions and how to coordinate these actions may be an advantage. Otherwise, team members must communicate their thoughts and ideas on the fly, which might be impossible due to time pressure, cognitive costs or noisy environments. This study examined if shared knowledge and verbal communication change through collective training. Forty-six under-18 and under-21 youth football players performed a football task in teams of two. The task consisted of passing and running elements common in football. After a training phase, and before two testing phases, players evaluated their actions and the actions of their assigned teammate regarding action type, location, and timing. Out of these evaluations, two indices of common understanding were computed. Furthermore, verbal communication during the task was video-and audio-recorded. Data analysis showed that shared knowledge considerably increased over time and with practice. Simultaneously, overall verbal communication and verbal communication consisting of orienting information was significantly reduced. Additionally, there was a tendency for a correlation that when shared knowledge increased, orienting verbal communication decreased. Overall, the players used orienting communications the most (77%). The study revealed that shared knowledge states and verbal communication change through collective training and that there might be a relation between the level of shared knowledge and the use of orienting verbal communication. Further studies in and off the field are needed to disentangle the complex interplay of team cognitions.
Neurotechnologies for Human Cognitive Augmentation: Current State of the Art and Future Prospects

Recent advances in neuroscience have paved the way to innovative applications that cognitively augment and enhance humans in a variety of contexts. This paper aims at providing a snapshot of the current state of the art and a motivated forecast of the most likely developments in the next two decades. Firstly, we survey the main neuroscience technologies for both observing and influencing brain activity, which are necessary ingredients for human cognitive augmentation. We also compare and contrast such technologies, as their individual characteristics (e.g., spatio-temporal resolution, invasiveness, portability, energy requirements, and cost) influence their current and future role in human cognitive augmentation. Secondly, we chart the state of the art on neurotechnologies for human cognitive augmentation, keeping an eye both on the applications that already exist and those that are emerging or are likely to emerge in the next two decades. Particularly, we consider applications in the areas of communication, cognitive enhancement, memory, attention monitoring/enhancement, situation awareness and complex problem solving, and we look at what fraction of the population might benefit from such technologies and at the demands they impose in terms of user training. Thirdly, we briefly review the ethical issues associated with current neuroscience technologies. These are important because they may differentially influence both present and future research on (and adoption of) neurotechnologies for human cognitive augmentation: an inferior technology with no significant ethical issues may thrive while a superior technology causing widespread ethical concerns may end up being outlawed. Finally, based on the lessons learned in our analysis, using past trends and considering other related forecasts, we attempt to forecast the most likely future developments of neuroscience technology for human cognitive augmentation and provide informed recommendations for promising future research and exploitation avenues.