Miracle-dz/UniFAR-FTUs huggingface dataset:
Animal experiments in biomedical research: Knowledge, self-evaluation and attitudes of biology and medical students

Animal experiments in biomedical research are debated in public, within the scientific community and among students. Despite increased efforts to reduce, refine and replace animal experiments, they remain integral components of the job of a biomedical scientist. In Germany, persons must have a university degree and adequate education and training to perform and direct animal experiments. Therefore, training courses such as FELASA (Federation of European Laboratory Animal Science Associations) courses are provided. However, in our experience, students become aware of this very late in their studies when decisions about their future careers have already been made. We initiated this study to have a better understanding of when and how animal experiments should be discussed during university education. We evaluated the knowledge, self-evaluation and attitudes of biology and medical students of different semesters regarding animal experiments at the RWTH Aachen University, Germany. An online survey was conducted to assess demographic information, knowledge about animal experiments, self-evaluation and attitudes towards animal experiments. Students of both fields showed limited knowledge of animal experiments. Biology students showed significantly better knowledge and self-evaluated their knowledge higher than medical students. The field of the study correlated with their knowledge and self-evaluation but did not predict participants’ attitudes towards animal experiments. In conclusion, the current study showed that there is still room for improvement to raise awareness about laboratory animal science in the biomedical research field.
Improve effluent water quality at Abu‐Rawash wastewater treatment plant with the application of coagulants

This research investigated a process to improve the Abu‐Rawash WWTP effluent water quality with the application of aluminum chloride (AlCl3); in turn, this improvement will lead to improve water quality at the El‐Rahawy drain and in the Rosetta branch of the Nile River. Sewage samples were collected from the effluent of the grit removal chamber. Jar tests were performed to estimate the coagulant dosage required to obtain acceptable treatment. To prove the efficiency of the AlCl3 in wastewater treatment, a comparison was conducted between AlCl3 and other common coagulants used in wastewater treatment which include ferrous sulfate (FeSO4), ferric sulfate (Fe2(SO4)3) and ferric chloride (FeCl3). Results showed AlCl3 was more cost‐effective and efficient in wastewater treatment than these three iron‐based coagulants. A paired‐sample t‐test was also performed to rank the performance of the various coagulants tested. The t‐test has also confirmed that the AlCl3 has the highest performance over those coagulants.
Dysbiosis index to evaluate the fecal microbiota in healthy cats and cats with chronic enteropathies

Objectives Previous studies have identified various bacterial taxa that are altered in cats with chronic enteropathies (CE) vs healthy cats. Therefore, the aim of this study was to develop a targeted quantitative molecular method to evaluate the fecal microbiota of cats. Methods Fecal samples from 80 client-owned healthy cats and 68 cats with CE were retrospectively evaluated. A panel of quantitative PCR (qPCR) assays was used to measure the fecal abundance of total bacteria and seven bacterial taxa: Bacteroides, Bifidobacterium, Clostridium hiranonis, Escherichia coli, Faecalibacterium, Streptococcus and Turicibacter. The nearest centroid classifier algorithm was used to calculate a dysbiosis index (DI) based on these qPCR abundances. Results The abundances of total bacteria, Bacteroides, Bifidobacterium, C hiranonis, Faecalibacterium and Turicibacter were significantly decreased, while those of E coli and Streptococcus were significantly increased in cats with CE (P <0.027 for all). The DI in cats with CE was significantly higher compared with healthy cats (P <0.001). When the cut-off value of the DI was set at 0, it provided 77% (95% confidence interval [CI] 66–85) sensitivity and 96% (95% CI 89–99) specificity to differentiate the microbiota of cats with CE from those of healthy cats. Fifty-two of 68 cats with CE had a DI >0. Conclusions and relevance A qPCR-based DI for assessing the fecal microbiota of cats was established. The results showed that a large proportion of cats with CE had an altered fecal microbiota as evidenced by an increased DI. Prospective studies are warranted to evaluate the utility of this assay for clinical assessment of feline CE.
Species composition and gear used in fishing during pre-monsoon period in the Shitalakshya river at Siddirgonj area, Narayangonj

The present investigation was conducted on the fish species composition and gear used in pre-monsoon period in the Shitalakshya river at Siddirgonj area, Narayangonj District. Personal interview with the fishermen was carried out for a period of twelve weeks from 1 February to 30 April, 2009. A total of 20 species of fishes belonging to 18 genera, under 10 families were identified in the catches of different nets. The highest numbers (10) of species were recorded in the catches of seine net and the lowest numbers (3) of species were recorded in case of moiya net. A total of 6 fishing gear types such as seine net (moshari ber jal), lift net (khora jal), lift net (veshal jal), setbag net (dur jal), gill net (current jal) and moiya net (moiya jal) were recorded from the study area. Fishing gears, like seine nets (moshari berjal) and gill net (current jal) were identified as destructive to local fish population.
External validation of the HIGH‐2‐LOW model: A predictive score for venous thromboembolism after allogeneic transplant

In patients undergoing hematopoietic cell transplantation (HCT), venous thromboembolism (VTE) remains a serious complication that lacks validated risk assessment models (RAMs) to guide thromboprophylaxis. To address this dilemma, we performed a temporal and external validation study of the recently derived HIGH‐2‐LOW RAM. We selected adult patients undergoing allogeneic HCT from Fred Hutchinson Cancer Research Center (FHCRC) and MD Anderson Cancer Center (MDACC). Patients who died, received anticoagulation, or did not engraft platelets by day 30 were excluded. Primary outcomes were defined as overall VTE and pulmonary embolism ± lower‐extremity deep venous thromboembolism (PE/LE‐DVT) by day 180. Covariates were weighted according to the original model, except that grade 2–4 GVHD was substituted for grade 3–4. Discrimination and calibration were assessed. A total of 765 patients from FHCRC and 954 patients from MDACC were included. Incident VTE by day 180 was 5.1% at FHCRC and 6.8% at MDACC. The HIGH‐2‐LOW score had a c‐statistic of 0.67 (0.59–0.75) for VTE and 0.75 (0.64–0.81) for PE/LE‐DVT at FHCRC and 0.62 (0.55–0.70) for VTE and 0.70 (0.56–0.83) for PE/LE‐DVT at MDACC. Twenty‐five percent and 23% of patients were classified as high risk (2+ points) in the two cohorts, respectively. High versus low‐risk was associated with odds ratio (OR) of 2.80 (1.46–5.38) for VTE and 4.21 (1.82–9.77) for PE/LE‐DVT at FHCRC and OR of 3.54 (2.12–5.91) for VTE and 6.82 (2.30–20.16) for PE‐LE‐DVT at MDACC. The HIGH‐2‐LOW RAM identified allogeneic HCT recipients at high risk for VTE in both validation cohorts. It can improve evidence‐based decision‐making for thromboprophylaxis post‐transplant.
PI3K activation allows immune evasion by promoting an inhibitory myeloid tumor microenvironment

Background Oncogenes act in a cell-intrinsic way to promote tumorigenesis. Whether oncogenes also have a cell-extrinsic effect on suppressing the immune response to cancer is less well understood. Methods We use an in vivo expression screen of known cancer-associated somatic mutations in mouse syngeneic tumor models treated with checkpoint blockade to identify oncogenes that promote immune evasion. We then validated candidates from this screen in vivo and analyzed the tumor immune microenvironment of tumors expressing mutant protein to identify mechanisms of immune evasion. Results We found that expression of a catalytically active mutation in phospho-inositol 3 kinase (PI3K), PIK3CA c.3140A>G (H1047R) confers a selective growth advantage to tumors treated with immunotherapy that is reversed by pharmacological PI3K inhibition. PIK3CA H1047R-expression in tumors decreased the number of CD8+ T cells but increased the number of inhibitory myeloid cells following immunotherapy. Inhibition of myeloid infiltration by pharmacological or genetic modulation of Ccl2 in PIK3CA H1047R tumors restored sensitivity to programmed cell death protein 1 (PD-1) checkpoint blockade. Conclusions PI3K activation enables tumor immune evasion by promoting an inhibitory myeloid microenvironment. Activating mutations in PI3K may be useful as a biomarker of poor response to immunotherapy. Our data suggest that some oncogenes promote tumorigenesis by enabling tumor cells to avoid clearance by the immune system. Identification of those mechanisms can advance rational combination strategies to increase the efficacy of immunotherapy.
Immediate impact of child maltreatment on mental, developmental, and physical health trajectories.

OBJECTIVE The immediate impact of child maltreatment on health and developmental trajectories over time is unknown. Longitudinal studies starting in the direct aftermath of exposure with repeated follow-up are needed. METHOD We assessed health and developmental outcomes in 6-month intervals over 2 years in 173 children, aged 3-5 years at study entry, including 86 children with exposure to emotional and physical abuse or neglect within 6 months and 87 nonmaltreated children. Assessments included clinician-administered, self- and parent-report measures of psychiatric and behavioral symptoms, development, and physical health. Linear mixed models and latent growth curve analyses were used to contrast trajectories between groups and to investigate the impact of maltreatment features on trajectories. RESULTS Maltreated children exhibited greater numbers of psychiatric diagnoses (b = 1.998, p < .001), externalizing (b = 13.29, p < .001) and internalizing (b = 11.70, p < .001) symptoms, impairments in cognitive (b = -11.586, p < .001), verbal (b = -10.687, p < .001), and motor development (b = -7.904, p = .006), and greater numbers of medical symptoms (b = 1.021, p < .001) compared to nonmaltreated children across all time-points. Lifetime maltreatment severity and/or age at earliest maltreatment exposure predicted adverse outcomes over time. CONCLUSION The profound, immediate, and stable impact of maltreatment on health and developmental trajectories supports a biological embedding model and provides foundation to scrutinize the precise underlying mechanisms. Such knowledge will enable the development of early risk markers and mechanism-driven interventions that mitigate adverse trajectories in maltreated children.
Not all mosquitoes are created equal: incriminating mosquitoes as vectors of arboviruses

The globalization of mosquito-borne arboviral diseases has placed more than half of the human population at risk. Understanding arbovirus ecology, including the role individual mosquito species play in virus transmission cycles, is critical for limiting disease. Canonical virus-vector groupings, such as Aedes- or Culex-associated flaviviruses, have historically been defined using phylogenetic associations, virus isolation in the field, and mosquito feeding patterns. These associations less frequently rely on vector competence, which quantifies the intrinsic ability of a mosquito to become infected with and transmit a virus during a subsequent blood feed. Herein, we quantitatively synthesize data from 80 laboratory vector competence studies of 115 mosquito-virus pairings of Australian mosquito species and viruses of public health concern to further substantiate existing canonical vector-virus groupings, uncover new associations, and quantify variation within these groupings. Our synthesis reinforces current canonical vector-virus groupings but reveals substantial variation within them. While Aedes species were generally the most competent vectors of canonical "Aedes-associated flaviviruses" (such as dengue, Zika, and yellow fever viruses), there are some notable exceptions; for example, Aedes notoscriptus is an incompetent vector of dengue viruses. Culex spp. were the most competent vectors of many traditionally Culex-associated flaviviruses including West Nile, Japanese encephalitis and Murray Valley encephalitis viruses, although some Aedes spp. are also moderately competent vectors of these viruses. Conversely, many mosquito genera were associated with the transmission of the arthritogenic alphaviruses, Ross River, Barmah Forest, and chikungunya viruses. We also confirm that vector competence is impacted by multiple barriers to infection and transmission within the mesenteron and salivary glands of the mosquito. Although these barriers represent important bottlenecks, species that were susceptible to infection with a virus were often likely to transmit it. Importantly, this synthesis provides essential information on what species need to be targeted in mosquito control programs.
Cultural adaptation of the person-centered maternity care scale at governmental health facilities in Cambodia

Background In Cambodia, the importance of valuing women’s childbirth experiences in improving quality of care has been understudied. This is largely because of absence of reliable Khmer tools for measuring women’s intrapartum care experiences. Generally, cross-cultural development of those tools often involves translation from a source language into a target language. Yet, few earlier studies considered Cambodian cultural context. Thus, we developed the Cambodian version of the Person-Centered Maternity Care (PCMC) scale, by culturally adapting its original to Cambodian context for ensuring cultural equivalence and content validity. Methods Three rounds of cognitive interviewing with 20 early postpartum women were conducted at two governmental health facilities in Cambodia. Cognitive interviewing was composed of structured questionnaire pretesting and qualitative probing. The issues identified in the process of transcribing and translating audio-recorded cognitive interviews were iteratively discussed among study team members, and further analyzed. Results A total of 14 issues related to cultural adaptations were identified in the 31 translated questions for the Cambodian version of the PCMC scale. Our study identified three key findings: (i) discrepancies between the WHO recommendations on intrapartum care and Cambodian field realities; (ii) discrepancies in recognition on PCMC between national experts and local women; and (iii) challenges in correctly collecting and interpreting less-educated women’s views on intrapartum care. Conclusion Not only women’s verbal data but also their non-verbal data and cultural contexts should be comprehensively counted, when reflecting Cambodian women’s intrapartum practice realities in the translated version. This is the first study that attempted to develop the tool for measuring Cambodian women’s experiences during childbirth, by addressing cross-cultural issues.
The Construction of Multi-ethnic Polygenic Risk Score using Transfer Learning

As most existing genome-wide association studies (GWAS) were conducted in European ancestry cohorts and as the existing PRS models have limited transferability across ancestry groups, PRS research on non-European ancestry groups is negatively impacted. Here we propose a novel PRS method using transfer learning techniques. Our approach, TL-PRS, uses gradient descent to fine-tune the baseline PRS model from an ancestry group with large sample GWAS to the dataset of target ancestry. In our application of constructing PRS for the six quantitative and two dichotomous traits for 10,285 South Asian and 8,168 African ancestry individuals in UK Biobank, TL-PRS achieved up to 42% average relative improvement compared to the existing methods. Our approach increases the transferability of PRSs across ancestries and thereby helps reduce existing inequities in genetics research.
Impact of Epstein-Barr virus co-infection on natural acquired Plasmodium vivax antibody response

Background: The simultaneous infection of Plasmodium falciparum and Epstein-Barr virus (EBV) could promote the development of the aggressive endemic Burkitt's Lymphoma (eBL) in children living in P. falciparum holoendemic areas. While it is well-established that eBL is not related to other human malaria parasites, the impact of EBV infection on the generation of human malaria immunity remains largely unexplored. Considering that this highly prevalent herpesvirus establishes a lifelong persistent infection on B-cells with possible influence on malaria immunity, we hypothesized that EBV co-infection could have impact on the naturally acquired antibody responses to P. vivax, the most widespread human malaria parasite. Methodology/Principal Findings: The study design involved three cross-sectional surveys at six-month intervals (baseline, 6 and 12 months) among long-term P. vivax exposed adults living in the Amazon rainforest. The approach focused on a group of malaria-exposed individuals whose EBV-DNA (amplification of balf-5 gene) was persistently detected in the peripheral blood (PersV DNA, n=27), and an age-matched malaria-exposed group whose EBV-DNA could never be detected during the follow-up (NegV DNA, n=29). During the follow-up period, the serological detection of EBV antibodies to lytic/latent viral antigens showed that IgG antibodies to viral capsid antigen (VCA-p18) were significantly different between groups (PersV DNA > NegV DNA ). A panel of blood-stage P. vivax antigens covering a wide range of immunogenicity confirmed that in general PersV DNA group showed low levels of antibodies as compared with NegV DNA. Interestingly, more significant differences were observed to a novel DBPII immunogen, named DEKnull-2, which has been associated with long-term neutralizing antibody response. Differences between groups were less pronounced with blood-stage antigens (such as MSP1-19) whose levels can fluctuate according to malaria transmission. Conclusions/Significance: In a proof-of-concept study we provide evidence that a persistent detection of EBV DNA in peripheral blood of adults in a P. vivax semi-immune population may impact the long-term immune response to major malaria vaccine candidates.
Practical Evaluation of Adversarial Robustness via Adaptive Auto Attack

Defense models against adversarial attacks have grown significantly, but the lack of practical evaluation methods has hindered progress. Evaluation can be defined as looking for defense models' lower bound of robustness given a budget number of iterations and a test dataset. A practical evaluation method should be convenient (i.e., parameter-free), efficient (i.e., fewer iterations) and reliable (i.e., approaching the lower bound of robustness). Towards this target, we propose a parameter-free Adaptive Auto Attack (A3) evaluation method which addresses the efficiency and reliability in a test-time-training fashion. Specifically, by observing that adversarial examples to a specific defense model follow some regularities in their starting points, we design an Adaptive Direction Initialization strategy to speed up the evaluation. Furthermore, to approach the lower bound of robustness under the budget number of iterations, we propose an online statistics-based discarding strategy that automatically identifies and abandons hard-to-attack images. Extensive experiments on nearly 50 widely-used defense models demonstrate the effectiveness of our A3. By consuming much fewer iterations than existing methods, i.e., 1/10 on average (10× speed up), we achieve lower robust accuracy in all cases. Notably, we won first place out of 1681 teams in CVPR 2021 White-box Adversarial Attacks on Defense Models competitions with this method. Code is available at: https://github.com/liuye6666/adaptive_auto_attack
projUNN: efficient method for training deep networks with unitary matrices

In learning with recurrent or very deep feed-forward networks, employing unitary matrices in each layer can be very effective at maintaining long-range stability. However, restricting network parameters to be unitary typically comes at the cost of expensive parameterizations or increased training runtime. We propose instead an efficient method based on rank-$k$ updates -- or their rank-$k$ approximation -- that maintains performance at a nearly optimal training runtime. We introduce two variants of this method, named Direct (projUNN-D) and Tangent (projUNN-T) projected Unitary Neural Networks, that can parameterize full $N$-dimensional unitary or orthogonal matrices with a training runtime scaling as $O(kN^2)$. Our method either projects low-rank gradients onto the closest unitary matrix (projUNN-T) or transports unitary matrices in the direction of the low-rank gradient (projUNN-D). Even in the fastest setting ($k=1$), projUNN is able to train a model's unitary parameters to reach comparable performances against baseline implementations. In recurrent neural network settings, projUNN closely matches or exceeds benchmarked results from prior unitary neural networks. Finally, we preliminarily explore projUNN in training orthogonal convolutional neural networks, which are currently unable to outperform state of the art models but can potentially enhance stability and robustness at large depth.
Self-consistency in $GW\Gamma$ formalism leading to quasiparticle-quasiparticle couplings

Within many-body perturbation theory, Hedin's formalism offers a systematic way to iteratively compute the self-energy $\Sigma$ of any interacting system, provided one can evaluate the interaction vertex $\Gamma$ exactly. This is however impossible in general, for it involves the functional derivative of $\Sigma$ with respect to the Green's function. Here, we analyze the structure of this derivative, splitting it into four contributions and outlining the type of quasiparticle interactions that each of them generate. Moreover we show how, in the implementation of self-consistency, the action of these contributions can be classified into two: a quantitative renormalization of previously included interaction terms, and the inclusion of qualitatively novel interaction terms through successive functional derivatives of $\Gamma$ itself, neglected until now. Implementing this latter type of self-consistency can extend the validity of Hedin's equations towards the high interaction limit, as we show in the example of the Hubbard dimer. Our analysis also provides a unifying perspective on the perturbation theory landscape, showing how the T-matrix approach is completely contained in Hedin's formalism.
Saturation of Ordered Graphs

Recently, the saturation problem of $0$-$1$ matrices gained a lot of attention. This problem can be regarded as a saturation problem of ordered bipartite graphs. Motivated by this, we initiate the study of the saturation problem of ordered and cyclically ordered graphs. We prove that dichotomy holds also in these two cases, i.e., for a (cyclically) ordered graph its saturation function is either bounded or linear. We also determine the order of magnitude for large classes of (cyclically) ordered graphs, giving infinite many examples exhibiting both possible behaviours, answering a problem of P\'alv\"olgyi. In particular, in the ordered case we define a natural subclass of ordered matchings, the class of linked matchings, and we start their systematic study, concentrating on linked matchings with at most three links and prove that many of them have bounded saturation function. In both the ordered and cyclically ordered case we also consider the semisaturation problem, where dichotomy holds as well and we can even fully characterize the graphs that have bounded semisaturation function.