Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Loci Controlling Parasite Load in Organs of Mice Infected With Leishmania major, Their Interactions and Sex Influence

Leishmaniasis is a serious health problem in many countries, and continues expanding to new geographic areas including Europe and USA. This disease, caused by parasites of Leishmania spp. and transmitted by phlebotomine sand flies, causes up to 1.3 million new cases each year and despite efforts toward its functional dissection and treatment it causes 20–50 thousands deaths annually. Dependence of susceptibility to leishmaniasis on sex and host's genes was observed in humans and in mouse models. Several laboratories defined in mice a number of Lmr (Leishmania major response) genetic loci that control functional and pathological components of the response to and outcome of L. major infection. However, the development of its most aggressive form, visceral leishmaniasis, which is lethal if untreated, is not yet understood. Visceral leishmaniasis is caused by infection and inflammation of internal organs. Therefore, we analyzed the genetics of parasite load, spread to internal organs, and ensuing visceral pathology. Using a new PCR-based method of quantification of parasites in tissues we describe a network-like set of interacting genetic loci that control parasite load in different organs. Quantification of Leishmania parasites in lymph nodes, spleen and liver from infected F2 hybrids between BALB/c and recombinant congenic strains CcS-9 and CcS-16 allowed us to map two novel parasite load controlling Leishmania major response loci, Lmr24 and Lmr27. We also detected parasite-controlling role of the previously described loci Lmr4, Lmr11, Lmr13, Lmr14, Lmr15, and Lmr25, and describe 8 genetic interactions between them. Lmr14, Lmr15, Lmr25, and Lmr27 controlled parasite load in liver and lymph nodes. In addition, Leishmania burden in lymph nodes but not liver was influenced by Lmr4 and Lmr24. In spleen, parasite load was controlled by Lmr11 and Lmr13. We detected a strong effect of sex on some of these genes. We also mapped additional genes controlling splenomegaly and hepatomegaly. This resulted in a systematized insight into genetic control of spread and load of Leishmania parasites and visceral pathology in the mammalian organism.
Transferable Interactiveness Knowledge for Human-Object Interaction Detection

Human-Object Interaction (HOI) Detection is an important problem to understand how humans interact with objects. In this paper, we explore Interactiveness Knowledge which indicates whether human and object interact with each other or not. We found that interactiveness knowledge can be learned across HOI datasets, regardless of HOI category settings. Our core idea is to exploit an Interactiveness Network to learn the general interactiveness knowledge from multiple HOI datasets and perform Non-Interaction Suppression before HOI classification in inference. On account of the generalization of interactiveness, interactiveness network is a transferable knowledge learner and can be cooperated with any HOI detection models to achieve desirable results. We extensively evaluate the proposed method on HICO-DET and V-COCO datasets. Our framework outperforms state-of-the-art HOI detection results by a great margin, verifying its efficacy and flexibility. Code is available at https://github.com/DirtyHarryLYL/Transferable-Interactiveness-Network.
Performance of a Dual Human Immunodeficiency Virus/Syphilis Rapid Test Compared to Conventional Serological Testing for Syphilis and HIV in a Laboratory Setting - Results of the Zimbabwe STI Etiology Study.

BACKGROUND Dual human immunodeficiency virus (HIV)/syphilis rapid, point-of-care testing may enhance syphilis screening among high risk populations, increase case finding, reduce time to treatment and prevent complications. We assessed the laboratory-based performance of a rapid dual HIV/syphilis test using serum collected from patients enrolled in the Zimbabwe Sexually Transmitted Infections (STI) Etiology study. METHODS Blood specimens were collected from patients presenting with STI syndromes in six, predominantly urban STI clinics in different regions of Zimbabwe. All specimens were tested at a central research laboratory using the Standard Diagnostics Bioline HIV/Syphilis Duo test. The treponemal syphilis component of the dual rapid test was compared to the Treponema pallidum haemagglutination assay (TPHA) as a gold standard comparator, both alone or in combination with a non-treponemal test, the rapid plasma reagin (RPR) test. The HIV component of the dual test was compared to a combination of HIV rapid tests conducted at the research laboratory following the Zimbabwe national HIV testing algorithm. RESULTS Of 600 men and women enrolled in the study, 436 consented to serological syphilis and HIV testing and had specimens successfully tested by all assays. The treponemal component of the dual test had a sensitivity of 66.2% (95% C.I.: 55.2% - 77.2%) and a specificity of 96.4% (95% C.I.: 94.5% - 98.3%) when compared to TPHA; the sensitivity increased to 91.7% (95% C.I.: 82.6% - 99.9%) when both TPHA and RPR were positive. The HIV component of the dual test had a sensitivity of 99.4% (95% C.I.: 98.4% - 99.9%) and a specificity of 100% (95% C.I. 99.9% - 100%) when compared to the HIV testing algorithm. CONCLUSION Laboratory performance of the SD Bioline HIV/Syphilis Duo test was high for the HIV component of the test. Sensitivity of the treponemal component was lower than reported from most laboratory-based evaluations in the literature. However, sensitivity of the test increased substantially among patients more likely to have active syphilis for which results of both standard treponemal and non-treponemal tests were positive.
Seoul Virus Tropism and Pathology in Naturally Infected Feeder Rats

Seoul virus (SEOV) is a zoonotic orthohantavirus carried by black and brown rats, and can cause hemorrhagic fever with renal syndrome in humans. Human cases of SEOV virus infection have most recently been reported in the USA, United Kingdom, France and the Netherlands and were primarily associated with contact with pet rats and feeder rats. Infection of rats results in an asymptomatic but persistent infection. Little is known about the cell tropism of SEOV in its reservoir and most available data is based on experimental infection studies in which rats were inoculated via a route which does not recapitulate virus transmission in nature. Here we report the histopathological analysis of SEOV cell tropism in key target organs following natural infection of a cohort of feeder rats, comprising 19 adults and 11 juveniles. All adult rats in this study were positive for SEOV specific antibodies and viral RNA in their tissues. One juvenile rat was seropositive, but negative in the rRT-PCR. Of the 19 adult rats of which subsequently additional organs were tested, SEOV RNA was detected in all lungs, followed by kidney (79%) and liver (74%). Histopathologic changes associated with SEOV infection were primarily found in the liver, consistent with a pathological diagnosis of a mild hepatitis. In conclusion, natural SEOV infection results in mild inflammation of the liver in the absence of clinical disease.
An Observational Link between AGN Eddington Ratio and [N ii]λ6583/Hα at 0.6 < z < 1.7

We present an observed relationship between the Eddington ratio (λEdd) and the optical narrow-emission-line ratio ([N ii]λ6583/Hα) of X-ray-selected broad-line active galactic nuclei (AGNs) at 0.6 < z < 1.7. We use 27 near-infrared spectra from the Fiber Multi-Object Spectrograph along with 26 sources from the literature. We show that the λEdd and [N ii]λ6583/Hα ratio at 0.6 < z < 1.7 exhibits a similar anti-correlation distribution of λEdd−[N ii]λ6583/Hα, as has been found for local ( ), ultra-hard, X-ray-selected AGNs. The observed distribution implies that there is a consistent relationship from local to z ∼ 1.7, which corresponds from the present time to 4 Gyr old. Further study of high-redshift, low-Eddington-ratio AGNs (log λEdd < −2) is necessary to determine fully whether the λEdd−[N ii]λ6583/Hα anti-correlation still holds in high-redshift AGNs at low Eddington ratios.
Differences Between the Prenatal Effects of Fluoxetine or Buspirone Alone or in Combination on Pain and Affective Behaviors in Prenatally Stressed Male and Female Rats

The selective serotonin reuptake inhibitor fluoxetine and the 5-HT1A receptor agonist buspirone are used to treat depression and anxiety. Previously we demonstrated that chronic stress during pregnancy (prenatal stress) in rats, used as a model of maternal depression risk, increased inflammatory pain and depressive-like behavior in the offspring; buspirone injected to pregnant dams was protective. Clinically, the addition of buspirone to fluoxetine increases the latter’s efficacy in treating depression in patients. Here, we investigated the influence of repeated prenatal injections of fluoxetine, buspirone or their combination on pain- and depressive-like behaviors in prenatally stressed young male and female rats. Prenatal stress augmented depressive-like behavior and both thermal and inflammatory pain (formalin test), replicating our prior findings, and increased basal levels of corticosterone in the blood plasma. Both drugs and their combination reduced the effects of prenatal stress on thermal pain and depressive-like behavior independently of sex. The combination of fluoxetine and buspirone, compared with fluoxetine, was more antinociceptive in the hot plate test in both sexes, and when compared with buspirone, was more antinociceptive only in males. A detailed study of the time-course of formalin-induced pain showed a nuanced effect of these drugs that was sex-dependent. The combination of the two drugs was less effective in females than males during the initial acute phase of nociceptive behavior in flexing + shaking behaviors, whereas that combination was more effective than fluoxetine alone in the first acute phase of licking behavior in females. The antinociceptive effect of buspirone dominated that of the drug combination and of fluoxetine alone, especially during the interphase of the formalin test in both sexes for both flexing + shaking and licking, suggesting a more effective prenatal action of buspirone on the development of a descending serotonergic inhibitory system modulating pain in the spinal cord dorsal horn neurons. Our results indicate that inflammatory pain-like responses integrated at the spinal level in males were more vulnerable to prenatal stress than females. In licking, the antinociceptive effect of fluoxetine and drug combination in the interphase was more in males than females. The data underscore the importance of considering sexual dimorphism when using drug therapy.
Repression of TERRA Expression by Subtelomeric DNA Methylation Is Dependent on NRF1 Binding

Chromosome ends are transcribed into long noncoding telomeric repeat-containing RNA (TERRA) from subtelomeric promoters. A class of TERRA promoters are associated with CpG islands embedded in repetitive DNA tracts. Cytosines in these subtelomeric CpG islands are frequently methylated in telomerase-positive cancer cells, and demethylation induced by depletion of DNA methyltransferases is associated with increased TERRA levels. However, the direct evidence and the underlying mechanism regulating TERRA expression through subtelomeric CpG islands methylation are still to establish. To analyze TERRA regulation by subtelomeric DNA methylation in human cell line (HeLa), we used an epigenetic engineering tool based on CRISPR-dCas9 (clustered regularly interspaced short palindromic repeats – dead CRISPR associated protein 9) associated with TET1 (ten-eleven 1 hydroxylase) to specifically demethylate subtelomeric CpG islands. This targeted demethylation caused an up-regulation of TERRA, and the enhanced TERRA production depended on the methyl-sensitive transcription factor NRF1 (nuclear respiratory factor 1). Since AMPK (AMP-activated protein kinase) is a well-known activator of NRF1, we treated cells with an AMPK inhibitor (compound C). Surprisingly, compound C treatment increased TERRA levels but did not inhibit AMPK activity in these experimental conditions. Altogether, our results provide new insight in the fine-tuning of TERRA at specific subtelomeric promoters and could allow identifying new regulators of TERRA.
Diffusion MRI: Assessment of the Impact of Acquisition and Preprocessing Methods Using the BrainVISA-Diffuse Toolbox

Diffusion MR images are prone to severe geometric distortions induced by head movement, eddy-current and inhomogeneity of magnetic susceptibility. Various correction methods have been proposed that depend on the choice of the acquisition settings and potentially provide highly different data quality. However, the impact of this choice has not been evaluated in terms of the ratio between scan time and preprocessed data quality. This study aims at investigating the impact of six well-known preprocessing methods, each associated to specific acquisition settings, on the outcome of diffusion analyses. For this purpose, we developed a comprehensive toolbox called Diffuse which automatically guides the user to the best preprocessing pipeline according to the input data. Using MR images of 20 subjects from the HCP dataset, we compared the six pre-processing pipelines regarding the following criteria: the ability to recover brain’s true geometry, the tensor model estimation and derived indices in the white matter, and finally the spatial dispersion of six well known connectivity pathways. As expected the pipeline associated to the longer acquisition fully repeated with reversed phase-encoding (RPE) yielded the higher data quality and was used as a reference to evaluate the other pipelines. In this way, we highlighted several significant aspects of other pre-processing pipelines. Our results first established that eddy-current correction improves the tensor-fitting performance with a localized impact especially in the corpus callosum. Concerning susceptibility distortions, we showed that the use of a field map is not sufficient and involves additional smoothing, yielding to an artificial decrease of tensor-fitting error. Of most importance, our findings demonstrate that, for an equivalent scan time, the acquisition of a b0 volume with RPE ensures a better brain’s geometry reconstruction and local improvement of tensor quality, without any smoothing of the image. This was found to be the best scan time/data quality compromise. To conclude, this study highlights and attempts to quantify the strong dependence of diffusion metrics on acquisition settings and preprocessing methods.
Gradual in vitro Evolution of Cefepime Resistance in an ST131 Escherichia coli Strain Expressing a Plasmid-Encoded CMY-2 β-Lactamase

Background In a previous report, a clinical ST131 Escherichia coli isolate (Ec-1),producing a plasmid-encoded AmpC β-lactamase CMY-2, evolved in vivo under cefepime (FEP) treatment to the FEP-resistant Ec-2 strain expressing an extended-spectrum β-lactamase CMY-33. To compare factors responsible for in vitro and in vivo FEP resistance, we reproduced in vitro FEP resistance evolution in Ec-1. Methods FEP-resistant mutants were generated by subjecting Ec-1 (FEP MIC = 0.125 mg/L) to sub-inhibitory concentrations of FEP. MICs were obtained by broth microdilution or Etest. Strains were sequenced on an Illumina HiSeq platform. Transcriptional levels and plasmid copy numbers were determined by real-time PCR. Outer membrane proteins (OMPs) were extracted and separated by SDS-PAGE. Growth kinetics was evaluated by measuring OD450. Results The CMY-2 expressed by Ec-1 evolved to a CMY-69 (strain EC-4) by an Ala294Pro substitution after 24 passages. After 30 passages, the FEP MIC increased to 256 mg/L (strain EC-32). SDS PAGE did not reveal any lack of OMPs in the mutant strains. However, blaCMY transcription levels were up to 14-times higher than in Ec-1, which was partially explained by mutations in the upstream region of repA resulting in a higher copy number of the blaCMY-harboring IncI1 plasmid. All mutants showed a slight growth defect but no significant difference in relative growth rates compared to Ec-1. Conclusion In vitro sub-inhibitory concentrations of FEP resulted in the selection of resistance mutations altering the H-10 helix of the CMY-2 and increasing the plasmid copy number. Appropriate dosing strategies may help preventing resistance evolution during treatments.
A Bottom Up Perspective to Understanding the Dynamics of Team Roles in Mission Critical Teams

There is a long history, dating back to the 50 s, which examines the manner in which team roles contribute to effective team performance. However, much of this work has been built on ad hoc teams working together for short periods of time under conditions of minimal stress. Additionally, research has been conducted with little attention paid to the importance of temporal factors, despite repeated calls for the importance of considering time in team research (e.g., Mohammed et al., 2009). To begin to understand team roles and how temporal aspects may impact the types of team roles employed when teams are working in extreme mission critical environments, the current manuscript uses a data-driven, bottom-up approach. Specifically, we employ the use of retrospective historical data as our input and a historiometric approach (Simonton, 2003). Source documents consist primarily of autobiographies, memoires, biographies, and first-hand accounts of crew interaction during spaceflight. Critical incidents regarding team interaction were extracted from these source documents and independently coded for team roles by two trained raters. Results of the study speak to the importance of task and social roles within teams that are predominantly intact and operating in extreme environments where mistakes can be life threatening. Evidence for the following task (i.e., coordinator, boundary spanner, team leader, evaluator, critic, information provider, team player, and innovator) and social roles (i.e., team builder, nurturer, harmonizer, entertainer, jokester, and the negative roles of attention seeker and negativist) were found. While it is often task roles that receive the greatest attention, results point to the importance of not neglecting the socioemotional health of the team (and the corresponding roles). Results also indicated that while some roles were consistently enacted independent of temporal considerations (e.g., mission length), the degree to which others were enacted varied across missions of differing lengths. Additionally, based on the current sample we see the following trends: (1) increased enactment of the team builder role as mission duration increases, (2) prominence of the entertainer role, and (3) increased emphasis on the visionary/problem solver role on missions over 2 years.
Partitioning and Selection of Data Consistency Mechanisms for Multicore Real-Time Systems

Multicore platforms are becoming increasingly popular in real-time systems. One of the major challenges in designing multicore real-time systems is ensuring consistent and timely access to shared resources. Lock-based protection mechanisms such as MPCP and MSRP have been proposed to guarantee mutually exclusive access in multicore systems at the expense of blocking. In this article, we consider partitioning and scheduling in multicore real-time systems with resource sharing. We first propose a resource-aware task partitioning algorithm for systems with lock-based protection. Wait-free methods, which ensure consistent access to shared memory resources with negligible blocking at the expense of additional memory space, are a suitable alternative when the shared resource is a communication buffer. We propose several approaches to solve the joint problem of task partitioning and the selection of a data consistency mechanism (lock-based or wait-free). The problem is first formulated as an Integer Linear Programming (ILP). For large systems where an ILP solution is not scalable, we propose two heuristic algorithms. Experimental results compare the effectiveness of the proposed approaches in finding schedulable systems with low memory cost and show how the use of wait-free methods can significantly improve schedulability.
FASTER Recurrent Networks for Video Classification

Video classification methods often divide the video into short clips, do inference on these clips independently, and then aggregate these predictions to generate the final classification result. Treating these highly-correlated clips as independent both ignores the temporal structure of the signal and carries a large computational cost: the model must process each clip from scratch. To reduce this cost, recent efforts have focused on designing more efficient clip-level network architectures. Less attention, however, has been paid to the overall framework, including how to benefit from correlations between neighboring clips and improving the aggregation strategy itself. In this paper we leverage the correlation between adjacent video clips to address the problem of computational cost efficiency in video classification at the aggregation stage. More specifically, given a clip feature representation, the problem of computing next clip's representation becomes much easier. We propose a novel recurrent architecture called FASTER for video-level classification, that combines high quality, expensive representations of clips, that capture the action in detail, and lightweight representations, which capture scene changes in the video and avoid redundant computation. We also propose a novel processing unit to learn integration of clip-level representations, as well as their temporal structure. We call this unit FAST-GRU, as it is based on the Gated Recurrent Unit (GRU). The proposed framework achieves significantly better FLOPs vs. accuracy trade-off at inference time. Compared to existing approaches, our proposed framework reduces the FLOPs by more than 10x while maintaining similar accuracy across popular datasets, such as Kinetics, UCF101 and HMDB51.
Differential Effects of Infant Vocalizations on Approach-Avoidance Postural Movements in Mothers

Infant vocalization plays a pivotal role in communicating infant mood to parents and thereby motivating parenting responses. Although many psychological and neural responses to infant vocalization have been reported, few studies have examined maternal approach-avoidance behavior in response to infant vocalization. Thus, this research sought to determine how infant emotional vocalization affects maternal behavior. Twenty mothers participated in this behavioral study, all of whom had infants of 24 months old or less. In the experiment, they stood on a Balance Board that collected real-time data regarding center of pressure (COP), while listening to a series of infant vocalizations including cry, laugh, and babbling. They then listened to the same vocalizations for a second time and rated their felt emotions in response to each vocalization. The participants demonstrated significant postural movements of approaching in response to cry stimuli or to stimuli regarded as highly urgent. In contrast, they demonstrated postural movement of avoidance in response to laugh vocalization. These findings suggest that parenting behavior in response to infant emotional vocalization is regulated not by the pleasant-unpleasant axis but by the urgency of the stimulus.