Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing SNP-markers to study population mixing and ecological adaptation in Baltic cod

Atlantic cod (Gadus morhua) is a species of great ecological and economical importance in the Baltic Sea. Here, two genetically differentiated stocks, the western and the eastern Baltic cod, display substantial mechanical mixing, hampering our understanding of cod ecology and impeding stock assessments and management. Based on whole-genome re-sequencing data from reference samples obtained from the study area, we designed two different panels of Single Nucleotide Polymorphisms markers (SNPs), which take into account the exceptional genome architecture of cod. A minimum panel of 20 diagnostic SNPs and an extended panel (20 diagnostic and 18 biologically informative SNPs, 38 in total) were developed and validated to distinguish unambiguously between the western and the eastern Baltic cod stocks and to enable studies of local adaptation to the specific environment in the Baltic Sea, respectively. We tested both panels on cod sampled from the southern Baltic Sea (n = 603) caught in 2015 and 2016. Genotyping results showed that catches from the mixing zone in the Arkona Sea, were composed of similar proportions of individuals of the western and the eastern stock. Catches from adjacent areas to the east, the Bornholm Basin and Gdańsk Deep, were exclusively composed of eastern Baltic cod, whereas catches from adjacent western areas (Belt Sea and Öresund) were composed of western Baltic cod. Interestingly, the two Baltic cod stocks showed strong genetic differences at loci associated with life-history trait candidate genes, highlighting the species’ potential for ecological adaptation even at small geographical scales. The minimum and the extended panel of SNP markers presented in this study provide powerful tools for future applications in research and fisheries management to further illuminate the mixing dynamics of cod in the Baltic Sea and to better understand Baltic cod ecology.
Learning Rich Part Hierarchies With Progressive Attention Networks for Fine-Grained Image Recognition

We investigate the localization of subtle yet discriminative parts for fine-grained image recognition. Based on the observation that such parts typically exist within a hierarchical structure (e.g., from a coarse-scale “head” to a fine-scale “eye” when recognizing bird species), we propose a novel progressive-attention convolutional neural network (PA-CNN) to progressively localize parts at multiple scales. The PA-CNN localizes parts in two steps, where a part proposal network (PPN) generates multiple local attention maps, and a part rectification network (PRN) learns part-specific features from each proposal and provides the PPN with refined part locations. This coupling of the PPN and PRN allows them to be optimized in a mutually reinforcing manner, leading to improved pinpointing of fine-grained parts. Moreover, the convolutional parameters for a PPN at a finer scale can be inherited from the PRN at a coarser scale, enabling a rich part hierarchy (e.g., eye and beak in a bird’s head) to be learned in a stacked fashion. Case studies show that PA-CNN can precisely identify parts without using bounding box/part annotations. In addition, quantitative evaluations demonstrate that PA-CNN yields state-of-the-art performance in three challenging fine-grained recognition tasks. i.e., CUB-2000–2011, FGVC-Aircraft, and Stanford Cars.
Vision-Based Freezing of Gait Detection With Anatomic Directed Graph Representation

Parkinson's disease significantly impacts the life quality of millions of people around the world. While freezing of gait (FoG) is one of the most common symptoms of the disease, it is time consuming and subjective to assess FoG for well-trained experts. Therefore, it is highly desirable to devise computer-aided FoG detection methods for the purpose of objective and time-efficient assessment. In this paper, in line with the gold standard of FoG clinical assessment, which requires video or direct observation, we propose one of the first vision-based methods for automatic FoG detection. To better characterize FoG patterns, instead of learning an overall representation of a video, we propose a novel architecture of graph convolution neural network and represent each video as a directed graph where FoG related candidate regions are the vertices. A weakly-supervised learning strategy and a weighted adjacency matrix estimation layer are proposed to eliminate the resource expensive data annotation required for fully supervised learning. As a result, the interference of visual information irrelevant to FoG, such as gait motion of supporting staff involved in clinical assessments, has been reduced to improve FoG detection performance by identifying the vertices contributing to FoG events. To further improve the performance, the global context of a clinical video is also considered and several fusion strategies with graph predictions are investigated. Experimental results on more than 100 videos collected from 45 patients during a clinical assessment demonstrated promising performance of our proposed method with an AUC of 0.887.
Effects of Sub-Acute Manganese Exposure on Thyroid Hormone and Glutamine (Gln)/Glutamate (Glu)-γ- Aminobutyric Acid (GABA) Cycle in Serum of Rats

Excessive manganese (Mn) exposure may adversely affect the central nervous system, and cause an extrapyramidal disorder known as manganism. The glutamine (Gln)/glutamate (Glu)–γ-aminobutyric acid (GABA) cycle and thyroid hormone system may be involved in Mn-induced neurotoxicity. However, the effect of Mn on the Gln/Glu–GABA cycle in the serum has not been reported. Herein, the present study aimed to investigate the effects of sub-acute Mn exposure on the Gln/Glu–GABA cycle and thyroid hormones levels in the serum of rats, as well as their relationship. The results showed that sub-acute Mn exposure increased serum Mn levels with a correlation coefficient of 0.733. Furthermore, interruption of the Glu/Gln–GABA cycle in serum was found in Mn-exposed rats, as well as thyroid hormone disorder in the serum via increasing serum Glu levels, and decreasing serum Gln, GABA, triiodothyronine (T3) and thyroxine (T4) levels. Additionally, results of partial correlation showed that there was a close relationship between serum Mn levels and the detected indicators accompanied with a positive association between GABA and T3 levels, as well as Gln and T4 levels in the serum of Mn-exposed rats. Unexpectedly, there was no significant correlation between serum Glu and the serum T3 and T4 levels. In conclusion, the results demonstrated that both the Glu/Gln–GABA cycle and thyroid hormone system in the serum may play a potential role in Mn-induced neurotoxicity in rats. Thyroid hormone levels, T3 and T4, have a closer relationship with GABA and Gln levels, respectively, in the serum of rats.
Strategies for engaging transgender populations in HIV prevention and care.

PURPOSE OF REVIEW Transgender (trans) populations are heavily impacted by HIV, yet face structural, social, and individual barriers to engagement in HIV prevention and care. In this review, we summarize the data on barriers and facilitators and discuss evidence-informed strategies to facilitate access to and engagement in HIV prevention and care by trans communities. RECENT FINDINGS Intersectional stigma and discrimination at structural, community, individual levels present substantial impediments to HIV prevention and optimal care. Access to gender-affirming health care is a priority for trans communities. Where trans communities are highly networked, these networks may provide a strong infrastructure for disseminating HIV innovations and reaching individuals who are not engaged in HIV services. Efforts to engage trans people in HIV prevention and care must address stigma, provide gender-affirming services, and build on community strengths and priorities to ensure trans populations achieve maximum benefit from advances in HIV prevention and care. SUMMARY Combination approaches that respond to the complex drivers of HIV in trans communities represent promising strategies for engaging trans people and their partners in HIV prevention and care.
Resistance Trends and Epidemiology of Citrobacter-Enterobacter-Serratia in Urinary Tract Infections of Inpatients and Outpatients (RECESUTI): A 10-Year Survey

Background and objectives: Urinary tract infections (UTIs) are the third most common infections in humans, representing a significant factor of morbidity, both among outpatients and inpatients. The pathogenic role of Citrobacter, Enterobacter, and Serratia species (CES bacteria) has been described in UTIs. CES bacteria present a therapeutic challenge due to the various intrinsic and acquired resistance mechanisms they possess. Materials and Methods: The aim of this study was to assess and compare the resistance trends and epidemiology of CES pathogens in UTIs (RECESUTI) in inpatients and outpatients during a 10-year study period. To evaluate the resistance trends of isolated strains, several antibiotics were chosen as indicator drugs based on local utilization data. 578 CES isolates were obtained from inpatients and 554 from outpatients, representing 2.57 ± 0.41% of all positive urine samples for outpatients and 3.02 ± 0.40% for inpatients. E. cloacae was the most prevalent species. Results: The ratio of resistant strains to most of the indicator drugs was higher in the inpatient group and lower in the second half of the study period. ESBL-producing isolates were detected in 0–9.75% from outpatient and 0–29.09% from inpatient samples. Conclusions: Resistance developments of CES bacteria, coupled with their intrinsic non-susceptibility to several antibiotics, severely limits the number of therapeutic alternatives, especially for outpatients.
Decreased Seroreactivity in Individuals Initiating Antiretroviral Therapy during Acute HIV Infection

Antiretroviral therapy (ART) during acute HIV infection (AHI) interrupts viral dynamics and may delay the emergence of serological markers targeted by current HIV screening and confirmatory assays, thus creating challenges for correctly classifying HIV infection status. ABSTRACT Antiretroviral therapy (ART) during acute HIV infection (AHI) interrupts viral dynamics and may delay the emergence of serological markers targeted by current HIV screening and confirmatory assays, thus creating challenges for correctly classifying HIV infection status. The performance of three HIV antigen/antibody combination (HIV Ag/Ab Combo) assays (the Bio-Rad GS, Abbott Architect, and Bio-Rad BioPlex 2200 assays) was evaluated with samples collected from RV254/South East Asia Research Collaboration in HIV 010 (RV254/SEARCH010) study (Bangkok, Thailand) participants at weeks 12 and 24 following the initiation of ART at Fiebig stage I (FI) (n = 23), FII (n = 39), or FIII/IV (n = 22). Supplemental, confirmatory testing was performed by the Geenius HIV 1/2 and HIV-1 Western blot assays (Bio-Rad). Samples from 30 untreated, HIV-1-infected individuals demonstrated robust HIV Ag/Ab Combo assay reactivity with well-developed HIV-1 Western blotting profiles by 24 weeks after infection. In contrast, 52.2% of samples from individuals initiating ART at FI, 7.7% of samples from individuals initiating ART at FII, and 4.5% of samples from individuals initiating ART at FIII/IV were nonreactive by the HIV Ag/Ab Combo assays, with 36.4 to 39.1% of samples having low signal-to-cutoff (S/CO) results by the Architect and BioPlex assays (S/CO < 10). Seroreversion from a reactive to a nonreactive status was observed in 10 individuals initiating ART at FII and 3 individuals initiating ART at FIII/IV. The Geenius and HIV-1 Western blot assay results were negative or indeterminate for 73.9% and 69.6% of individuals, respectively, treated at FI; 50.0% and 26.3% of individuals, respectively, treated at FII; and 54.5% and 40.9% of individuals, respectively, treated at FIII/IV. Virologic suppression of HIV-1 by ART during AHI impedes seroconversion to biomarkers of infection, limiting the utility of HIV Ag/Ab Combo and supplemental, confirmatory assays for infection status determination.
Singular angular magnetoresistance in a magnetic nodal semimetal

Mind the angle Interplay between real- and momentum-space properties of materials can lead to exotic phenomena. Suzuki et al. studied electrical transport in the presence of a magnetic field in cerium-aluminum-germanium, a Weyl semimetal that also harbors magnetism (see the Perspective by Hassinger and Meng). As they varied the orientation of the applied field, they noticed spikes of resistivity sharply centered around the high symmetry axes of the material. The spikes were a consequence of the small overlap of Fermi surfaces—which “live” in momentum space—on either side of magnetic domain walls, which occur in real space. This extreme angular sensitivity may be useful in practical applications. Science, this issue p. 377; see also p. 324 Transport measurements show extreme sensitivity to the angle of the applied magnetic field in CeAlGe. Transport coefficients of correlated electron systems are often useful for mapping hidden phases with distinct symmetries. Here we report a transport signature of spontaneous symmetry breaking in the magnetic Weyl semimetal cerium-aluminum-germanium (CeAlGe) system in the form of singular angular magnetoresistance (SAMR). This angular response exceeding 1000% per radian is confined along the high-symmetry axes with a full width at half maximum reaching less than 1° and is tunable via isoelectronic partial substitution of silicon for germanium. The SAMR phenomena is explained theoretically as a consequence of controllable high-resistance domain walls, arising from the breaking of magnetic point group symmetry strongly coupled to a nearly nodal electronic structure. This study indicates ingredients for engineering magnetic materials with high angular sensitivity by lattice and site symmetries.
“But I did not touch nobody!”—Patients' and nurses' perspectives and recommendations after aggression on psychiatric wards—A qualitative study

Abstract Aims To gain a deeper understanding of the differences in patients and staff perspectives in response to aggression and to explore recommendations on prevention. Design Qualitative, grounded theory study. Methods We conducted semi‐structured interviews with patients and nurses involved in an aggressive incident. Data collection was performed from May 2016 ‐ March 2017. Results Thirty‐one interviews were conducted concerning 15 aggressive incidents. Patients and nurses generally showed agreement on the factual course of events, there was variation in agreement on the perceived severity (PS). Patients' recommendations on prevention were mostly personally focussed, while nurses suggested general improvements. Conclusion Patients are often capable to evaluate aggression and give recommendations on prevention shortly after the incident. Patients and nurses differ in the PS of aggression. Recommendations on prevention of patients and nurses are complementary. Impact What problem did the study address? Perspectives of patients and nurses differ with respect to aggression, but how is unclear. What were the main findings? Patients and nurses generally described a similar factual course of events concerning the incident, patients often perceive the severity less than nurses. Patients are capable to give recommendations on prevention of aggressive incidents, shortly after the incident. Where and on whom will the research have impact? Factual course of events can be a common ground to start evaluating aggressive incidents and post‐incident review should address the severity of incidents. Asking recommendations from patients on how to improve safety and de‐escalation can lead to innovative and personal de‐escalation strategies and supports patients autonomy.
Structure of the saxiphilin:saxitoxin (STX) complex reveals a convergent molecular recognition strategy for paralytic toxins

Bullfrog saxiphilin:STX complex defines a toxin “molecular sponge” blueprint for STX recognition and toxin resistance. Dinoflagelates and cyanobacteria produce saxitoxin (STX), a lethal bis-guanidinium neurotoxin causing paralytic shellfish poisoning. A number of metazoans have soluble STX-binding proteins that may prevent STX intoxication. However, their STX molecular recognition mechanisms remain unknown. Here, we present structures of saxiphilin (Sxph), a bullfrog high-affinity STX-binding protein, alone and bound to STX. The structures reveal a novel high-affinity STX-binding site built from a “proto-pocket” on a transferrin scaffold that also bears thyroglobulin domain protease inhibitor repeats. Comparison of Sxph and voltage-gated sodium channel STX-binding sites reveals a convergent toxin recognition strategy comprising a largely rigid binding site where acidic side chains and a cation-π interaction engage STX. These studies reveal molecular rules for STX recognition, outline how a toxin-binding site can be built on a naïve scaffold, and open a path to developing protein sensors for environmental STX monitoring and new biologics for STX intoxication mitigation.
Next-generation Sequencing Study of Pathogens in Serum from Patients with Febrile Jaundice in Sierra Leone.

OBJECTIVE People in Western Africa suffer greatly from febrile jaundice, which is caused by a variety of pathogens. However, yellow fever virus (YFV) is the only pathogen under surveillance in Sierra Leone owing to the undeveloped medical and public health system there. Most of the results of YFV identification are negative. Elucidation of the pathogen spectrum is required to reduce the prevalence of febrile jaundice. METHODS In the present study, we used Ion Torrent semiconductor sequencing to profile the pathogen spectrum in archived YFV-negative sera from 96 patients in Sierra Leone who presented with unexplained febrile jaundice. RESULTS The most frequently identified sequencing reads belonged to the following pathogens: cytomegalovirus (89.58%), Epstein-Barr virus (55.21%), hepatitis C virus (34.38%), rhinovirus (28.13%), hepatitis A virus (20.83%), coxsackievirus (10.42%), Ebola virus (8.33%), hepatitis E virus (8.33%), lyssavirus (4.17%), leptospirosis (4.17%), chikungunya virus (2.08%), Crimean-Congo hemorrhagic fever virus (1.04%), and hepatitis B virus (1.04%). CONCLUSION The distribution of sequencing reads suggests a broader spectrum of pathogens for consideration in clinical diagnostics and epidemiological surveillance in Sierra Leone.
A randomized study comparing regular care with a nurse‐led clinic based on tight disease activity control and person‐centred care in patients with rheumatoid arthritis with moderate/high disease activity: A 6‐month evaluation

Abstract Introduction A recent survey showed that 27% of rheumatoid arthritis (RA) patients had inadequately controlled disease activity. Hence, there is a need for new strategies aiming at improving patient outcomes. The aim of the present study was to evaluate the effect of a nurse‐led clinic with frequent visits, treat‐to‐target and person‐centred care of patients with established RA and moderate‐to‐high disease activity compared with patients receiving regular care. Methods The study was a randomized, controlled trial over 26 weeks, with a nonrandomized extension to week 50. Patients were randomized to an intervention group (IG; nurse‐led clinic) based on person‐centred care, frequent visits and “treat to target”, or to a control group (CG) which visited the clinic according to care as usual. The primary outcome was the difference in the DAS28 change between the IG and the CG groups. Results A total of 332 patients were screened for eligibility, of which 70 were randomly assigned to either the IG (n = 36) or the CG (n = 34) group. The primary outcome was not met, although patients in the IG group tended to improve more than those in the CG group (difference: 0.43 (95% confidence interval [CI] –0.27, 1.13). In both the IG and CG groups, delta‐DAS28 improved significantly. The European League Against Rheumatology moderate or good response was achieved by 76% (95% CI 58, 89) in the IG and 49% (95% CI 32, 65) in the CG group. Conclusions Disease activity tended to improve more with the nurse‐led intervention compared with regular care, although the difference was not significant, probably partly due to the lack of statistical power.
Transapical transcatheter aortic valve replacement with the balloon expandable aortic bioprosthetic valve in high risk patients with severe aortic stenosis: Intermediate-term results from the register of the clinic of cardiac surgery.

BACKGROUND The purpose of this study is to report our experience in performing transapical (TA) TAVR with a balloon-expandable valve only by cardiac surgeons, with on site interventional cardiology support. METHODS A retrospective review of 97 consecutive patients that underwent TA TAVR due to severe symptomatic aortic stenosis was performed from 2012 to 2016. Median follow-up time was 20.5 months. Preoperative risk factors and postoperative outcomes were evaluated using Valve Academic Research Consortium-2 definitions. RESULTS All patients were high risk with a mean Euroscore of 7.28±7.77. Five year and 30-day mortality were 9.3 % and 1.1 %, respectively. Ninty six (98.9 %) of the patients had no or mild paravalvular leak seen by transesophageal echocardiography after implantation. Device success was 91.8%. Postoperatively there was a significant increase of the ejection fraction (50.8±7.1 % preoperatively vs 53.1±7.7 % postoperatively, p=0.009) and reverse remodeling of the left ventricle (left ventricular end-diastolic diameter preoperatively 50.8±7.1 mm vs 49.2±8.1 mm postoperatively, p=0.031). CONCLUSION Our experience demonstrates that TA TAVR can be performed only by cardiac surgeons, with on site interventional cardiology support safely and successfully with low and comparable postoperative mortality and rate of complications (Tab. 4, Fig. 1, Ref. 26).
Prediction of dosimetric accuracy for VMAT plans using plan complexity parameters via machine learning.

PURPOSE The dosimetric accuracies of volumetric modulated arc therapy (VMAT) plans were predicted using plan complexity parameters via machine learning. METHODS The dataset consisted of 600 cases of clinical VMAT plans from a single institution. The predictor variables (n = 28) for each plan included complexity parameters, machine type, and photon beam energy. Dosimetric measurements were performed using a helical diode array (ArcCHECK), and the dosimetric accuracy of the passing rates for a 5% dose difference (DD5%) and gamma index of 3%/3 mm (γ3%/3 mm) were predicted using three machine learning models: regression tree analysis (RTA), multiple regression analysis (MRA), and neural networks (NNs). First, the prediction models were applied to 500 cases of the VMAT plans. Then, the dosimetric accuracy was predicted using each model for the remaining 100 cases (evaluation dataset). The error between the predicted and measured passing rates was evaluated. RESULTS For the 600 cases, the mean ± standard deviation of the measured passing rates were 92.3 ± 9.1% and 96.8 ± 3.1% for DD5% and γ3%/3 mm, respectively. For the evaluation dataset, the mean ± standard deviation of the prediction errors for DD5% and γ3%/3 mm were 0.5 ± 3.0% and 0.6 ± 2.4% for RTA, 0.0 ± 2.9% and 0.5 ± 2.4% for MRA, and -0.2 ± 2.7% and -0.2 ± 2.1% for NN, respectively. CONCLUSIONS NNs performed slightly better than RTA and MRA in terms of prediction error. These findings may contribute to increasing the efficiency of patient-specific quality-assurance procedures. This article is protected by copyright. All rights reserved.