Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk factors of HIV and variation in access to clean needles among people who inject drugs in Pakistan

ABSTRACT We identified key risk factors for HIV among people who inject drugs (PWID) in Pakistan and explored access to free clean needles. Multivariable logistic regression was used to investigate associations between HIV prevalence and demographic, behavioral, and socio-economic characteristics of PWID. Data came from the Government of Pakistan’s Integrated Biological and Behavioral Surveillance (IBBS) Round 5 (2016–17; 14 cities). A secondary analysis investigated associations with reported access to clean needles. Unweighted HIV prevalence among 4,062 PWID (99% male) was 21.0%. Longer injecting duration (Odds ratio [OR] 1.06 [95% confidence interval: 1.02–1.10]; per year), higher injecting frequency (OR 1.67 [1.30–2.13]; per unit increase), and injecting heroin (OR 1.90 [1.11–3.25]) were positively associated with HIV prevalence. There was no association between using a used syringe at last injection and HIV. Having>10 years of education had lower odds of HIV than being illiterate (OR 0.58 [0.35–0.95]). Having a regular sexual partner (OR 0.74 [0.57–0.97]) or paying for sex with the opposite sex (OR = 0.62 [0.45–0.85]) had lower odds of HIV than not. Conversely, PWID paying a man/hijra for sex had higher odds of HIV (OR 1.20 [1.00–1.43]). Receipt of clean needles varied by city of residence (0–97% coverage), whilst PWID with knowledge of HIV service delivery programs had higher odds of receiving clean needles (OR 4.58 [3.50–5.99]). Injecting behaviors were associated with HIV prevalence among PWID, though risks related to paying for sex remain complicated. Geographical variation in access to clean needles suggests potential benefits of more widely spread public health services. Key Messages What is already known on this topic The HIV epidemic in Pakistan is concentrated among key populations including people who inject drugs. What this study adds Injecting practices, sexual behaviors, and socio-economic factors are associated with HIV prevalence among people who inject drugs. Access to harm reduction services is varied in Pakistan. How this study might affect research, practice, or policy Access to clean free needles, as well as service delivery programs, with a broad geographical reach remain important to curb the HIV epidemic among people who inject drugs in Pakistan.
Dynamics of a Spinning Rocket with Internal Mass Flow

One of the main simplifying assumptions made in the study of the attitude motions of a rocket-type variable mass system is that the motion of the fluid products of combustion relative to the rocket body, as these fluid particles exit the rocket's combustion chamber, remains symmetric with re- spect to the rocket axis, and the fluid particles have no transverse motion relative to the rocket body. This assumption brings about a tremendous sim- plification of the equations that govern the attitude motion of a rocket, and is thus very attractive. Yet, one recognizes that such an assumption becomes questionable if the rocket body is allowed to spin. This paper examines the validity of this common assumption. The paper attempts to reconstruct what is lost when this assumption is made, and quantifies the effects on attitude dynamics predictions. Results obtained show that this assumption is in fact reasonable. Although internal fluid whirling motion can cause deviations in spin rate predictions, the actual effects are not dramatic. There is a noticeable impact on the frequencies of the transverse angular velocity components, but the amplitude of the transverse angular velocity vector is largely unaffected.
A novel image-based method for simultaneous counting of Lactobacillus and Saccharomyces in mixed culture fermentation

Abstract Mixed microorganism cultures are prevalent in the food industry. A variety of microbiological mixtures have been used in these unique fermenting processes to create distinctive flavor profiles and potential health benefits. Mixed cultures are typically not well characterized, which may be due to the lack of simple measurement tools. Image-based cytometry systems have been employed to automatically count bacteria or yeast cells. In this work, we aim to develop a novel image cytometry method to distinguish and enumerate mixed cultures of yeast and bacteria in beer products. Cellometer X2 from Nexcelom was used to count of Lactobacillus plantarum and Saccharomyces cerevisiae in mixed cultures using fluorescent dyes and size exclusion image analysis algorithm. Three experiments were performed for validation. (1) Yeast and bacteria monoculture titration, (2) mixed culture with various ratios, and (3) monitoring a Berliner Weisse mixed culture fermentation. All experiments were validated by comparing to manual counting of yeast and bacteria colony formation. They were highly comparable with ANOVA analysis showing p-value > 0.05. Overall, the novel image cytometry method was able to distinguish and count mixed cultures consistently and accurately, which may provide better characterization of mixed culture brewing applications and produce higher quality products.
Assessing Potential Habitat for Freshwater Mussels by Transferring a Habitat Suitability Model within the Ozark Ecoregion, Missouri

ABSTRACT Habitat suitability models for freshwater mussels can inform conservation of these imperiled animals. Riverscape-scale hydrogeomorphic variables were previously used to predict suitable mussel habitat in the Meramec River basin, Missouri. We evaluated transferability of the Meramec River habitat suitability model to the Gasconade and Little Black rivers, in the Ozark Highlands ecoregion, Missouri. The best-fit models relied on transferring and adapting the original modeling framework to better represent the unique habitat characteristics of each river. Mussel bed occurrence in both rivers was associated with reaches that were classified as pools. Mussel beds in the Gasconade River were also associated with laterally stable reaches adjacent to small bluffs, distant from gravel bars, and with higher stream power indices. Mussel beds in the Little Black River were associated with reaches with higher surface water availability during low-flow conditions, lower stream power indices, and bluffs located downstream. Our results show that existing habitat models can be transferred to other streams with similar environmental conditions, but differences in watershed characteristics can affect transferability.
Enhanced performance of HTS hairpin type bandpass filter by interdigitated inner poles

To improve the performance of the hairpin type bandpass filter, we designed a new style hairpin type HTS 2-pole microstrip bandpass filter by using interdigitated inner poles. The filter was designed to operate at 5.8 GHz. The interdigitated inner pole has 29 fingers where each finger had a dimension of 0.4 mm length and 0.1 mm width. The gap distance between the two fingers was 0.1 mm. In simulations, the new style filter showed a significant improvement in the performance over the regular hairpin type filter. To fabricate the filters by using superconductive YBa/sub 2/Cu/sub 3/O/sub 7-x/ films, we deposited the films on the sapphire substrates by using CeO/sub 2/ thin layer as a buffer layer. We used ArF pulsed laser deposition system to fabricate the films. We used ArF to obtain the smoother film surface instead of KrF that has been used more widely. We also rotated the substrates during the film growth to obtain the better film uniformity. Fabricated YBa/sub 2/Cu/sub 3/O/sub 7-x/ films showed a critical temperature of 87.8 K. The packaged filter with the size of 13.7 mm/spl times/3.3 mm showed lower center frequency, narrower bandwidth, and less loss compared to the same size regular hairpin type filter, by 14.5%, 29.6%, 0.55 dB, respectively.
Robust ℋ︁2 static output feedback design starting from a parameter‐dependent state feedback controller for time‐invariant discrete‐time polytopic systems

This paper investigates the problem of computing robust ℋ︁2 static output feedback controllers for discrete‐time uncertain linear systems with time‐invariant parameters lying in polytopic domains. A two stages design procedure based on linear matrix inequalities is proposed as the main contribution. First, a parameter‐dependent state feedback controller is synthesized and the resulting gains are used as an input condition for the second stage, which designs the desired robust static output feedback controller with an ℋ︁2 guaranteed cost. The conditions are based on parameter‐dependent Lyapunov functions and, differently from most of existing approaches, can also cope with uncertainties in the output control matrix. Numerical examples, including a mass–spring system, illustrate the advantages of the proposed procedure when compared with other methods available in the literature. Copyright © 2009 John Wiley & Sons, Ltd.
PrivExtractor: Toward Redressing the Imbalance of Understanding between Virtual Assistant Users and Vendors

The use of voice-controlled virtual assistants (VAs) is significant, and user numbers increase every year. Extensive use of VAs has provided the large, cash-rich technology companies who sell them with another way of consuming users’ data, providing a lucrative revenue stream. Whilst these companies are legally obliged to treat users’ information “fairly and responsibly,” artificial intelligence techniques used to process data have become incredibly sophisticated, leading to users’ concerns that a lack of clarity is making it hard to understand the nature and scope of data collection and use. There has been little work undertaken on a self-contained user awareness tool targeting VAs. PrivExtractor, a novel web-based awareness dashboard for VA users, intends to redress this imbalance of understanding between the data “processors” and the user. It aims to achieve this using the four largest VA vendors as a case study and providing a comparison function that examines the four companies’ privacy practices and their compliance with data protection law. As a result of this research, we conclude that the companies studied are largely compliant with the law, as expected. However, the user remains disadvantaged due to the ineffectiveness of current data regulation that does not oblige the companies to fully and transparently disclose how and when they use, share, or profit from the data. Furthermore, the software tool developed during the research is, we believe, the first that is capable of a comparative analysis of VA privacy with a visual demonstration to increase ease of understanding for the user.
The Epidemiology of Suicide in London

The paper considers trends in the incidence of suicide in London in relation to national trends and highlights the distinctive fall in its suicide levels. Within London differentials across boroughs and wards are investigated, with particular regard to contextual variability across subpopulations in the impact of social deprivation and social fragmentation (anomie). Patterns of causation also differ for suicide disaggregated by age group and sex. The relevance of these differentials for explaining the distinctive trend in London's overall suicide rate is discussed.
The Relationship between Eccentric and Concentric Measures of Ankle Strength and Functional Equinus in Classical Dancers

Classically trained dancers possess a supernormal range of motion in ankle plantar flexion with a reciprocally diminished range of motion in ankle dorsiflexion. Restricted joint motion is considered homologous with diminished strength in muscle groups associated with the lost motion and is associated with compensatory hypermobility in neighboring joints. The purpose of this study was to measure clinical and functional ranges of ankle motion and to assess peak torque values for ankle plantar flexion and dorsiflexion collected both eccentrically and concentrically. Twelve professional, classical dancers (6 males, 6 females) were measured goniometrically for ankle range of motion using three different positioning techniques and for isokinetic peak torques of ankle plantar flexion (PF) and dorsiflexion (DF) at two different joint angles and two different speeds. Measured by traditional goniometric techniques, ankle dorsiflexion was limited relative to published norms and significantly lower than measures taken when the dancer assumed a functional testing position. A relationship of moderate strength between dorsiflexion range and peak torque values was obtained, although it did not meet our criterion for significance. No significant differences were seen in either gender between concentric and eccentric measures of ankle strength for any of the testing conditions. The equality of concentric and eccentric measures may reflect a training effect resulting from regularly practiced concentric relevé activities or may be a result of limitations in the laboratory setting.
Dance Injuries in the Older Dancer

From a group of 727 consecutive injured dancers and dance teachers, 66 were 45 years of age or older. The injuries and physical complaints of these older dancers were analyzed. They were compared with the data of a control group of 345 consecutive injured dancers of all ages from a previous study. In approximately 75% of the injuries in both groups, the lower extremity was involved. There was a large as yet unexplained difference in the percentage of ankle injuries in the two groups: 27% in the younger group and only 3% in the older group. Almost half of the injuries in the older group were due to degenerative changes, most often of the patellofemoral joint.
Management of Injuries in the Young Dancer

Individuals involved in the care of the young dancer must understand the etio-logic effects of growth, flexibility, and anatomical alignment on injuries. This article presents an approach to injuries in young dancers and discusses some specific injuries, particularly involving the lower extremities and the spine. Aspects of injury assessment and prevention include attention to each dancer's specific anatomy, proper technique, careful progression of skills, and monitoring the volume and intensity of dance training. Management of the dancer begins with identifying the specific anatomic diagnosis. It is important to be familiar with the demands of dance and the patterns of pain commonly associated with specific injuries. This knowledge helps differentiate between injuries that may be treated non-operatively from those that require further investigations and interventions.
The Relationship between Imagery and Competitive Anxiety in Ballet Auditions

Aligned with competitive anxiety research in athletics, this study explored audition anxiety and the role of imagery in the anxiety-performance relationship among 131 female auditioning ballet dancers. A better understanding of how auditioning dancers experience anxiety and associated image content can help train dancers preparing for anxiety-provoking, high-stakes performances. The CSAI-2 assessing competitive state anxiety and confidence and the SIQ assessing the cognitive and motivational functions of imagery were slightly modified for administration in the audition context. The MIQ-R was used to assess movement imagery. All instrument subscales, with the exception of the CG-Strategies subscale of the SIQ, demonstrated adequate internal consistency. Ballet dancers’ scores were similar to those reported by aesthetic sport athletes. Obtaining a position with a dance company was used as a proxy for defining success. Successful dancers with prior audition success were more confident than those without prior success and unsuccessful dancers with, and without, prior success. As a group, successful dancers experienced less cognitive anxiety and more somatic anxiety than unsuccessful dancers. Although imagery ability and image content did not differentiate dancers by performance, confident dancers had higher kinesthetic imagery ability and used more mastery and less arousal imagery than less confident dancers. In contrast, cognitively and somatically anxious dancers used less mastery and more arousal imagery. The athletic paradigm appears to be an appropriate framework for studying performance-related anxiety among dancers. Dancers and practitioners are encouraged to focus on mastery images for increasing confidence and decreasing anxiety. Dancers with prior audition success may be incorporating theses experiences in generating arousal imagery shown to predicted somatic anxiety, anxiety that does not appear to be detrimental to performance when cognitive anxiety is controlled.
Emergence of power-law distributions in protein-protein interaction networks through study bias

Protein-protein interaction (PPI) networks have been found to be power-law-distributed, i. e. , in observed PPI networks, the fraction of nodes with degree k often follows a power-law (PL) distribution k-α. The emergence of this property is typically explained by evolutionary or functional considerations. However, the experimental procedures used to detect PPIs are known to be heavily affected by technical and study bias. For instance, proteins known to be involved in cancer are often heavily overstudied and proteins used as baits in large-scale experiments tend to have many false-positive interaction partners. This raises the question whether PL distributions in observed PPI networks could be explained by these biases alone. Here, we address this question using statistical analyses of the degree distributions of 1000s of observed PPI networks of controlled provenance as well as simulation studies. Our results indicate that study bias and technical bias can indeed largely explain the fact that observed PPI networks tend to be PL-distributed. This implies that it is problematic to derive hypotheses about the degree distribution and emergence of the true biological interactome from the PL distributions in observed PPI networks.
A machine-readable specification for genomics assays

Understanding the structure of sequenced fragments from genomics libraries is essential for accurate read preprocessing. Currently, different assays and sequencing technologies require custom scripts and programs that do not leverage the common structure of sequence elements present in genomics libraries. We present seqspec, a machine-readable specification for libraries produced by genomics assays that facilitates standardization of preprocessing and enables tracking and comparison of genomics assays. The specification and associated seqspec command line tool is available at https://github.com/IGVF/seqspec.
OASIS: An interpretable, finite-sample valid alternative to Pearson’s X2 for scientific discovery

Contingency tables, data represented as counts matrices, are ubiquitous across quantitative research and data-science applications. Existing statistical tests are insufficient however, as none are simultaneously computationally efficient and statistically valid for a finite number of observations. In this work, motivated by a recent application in reference-free genomic inference (1), we develop OASIS (Optimized Adaptive Statistic for Inferring Structure), a family of statistical tests for contingency tables. OASIS constructs a test-statistic which is linear in the normalized data matrix, providing closed form p-value bounds through classical concentration inequalities. In the process, OASIS provides a decomposition of the table, lending interpretability to its rejection of the null. We derive the asymptotic distribution of the OASIS test statistic, showing that these finitesample bounds correctly characterize the test statistic’s p-value up to a variance term. Experiments on genomic sequencing data highlight the power and interpretability of OASIS. The same method based on OASIS significance calls detects SARS-CoV-2 and Mycobacterium Tuberculosis strains de novo, which cannot be achieved with current approaches. We demonstrate in simulations that OASIS is robust to overdispersion, a common feature in genomic data like single cell RNA-sequencing, where under accepted noise models OASIS still provides good control of the false discovery rate, while Pearson’s X2 test consistently rejects the null. Additionally, we show on synthetic data that OASIS is more powerful than Pearson’s X2 test in certain regimes, including for some important two group alternatives, which we corroborate with approximate power calculations. Significance Statement Contingency tables are pervasive across quantitative research and data-science applications. Existing statistical tests fall short, however; none provide robust, computationally efficient inference and control Type I error. In this work, motivated by a recent advance in reference-free inference for genomics, we propose a family of tests on contingency tables called OASIS. OASIS utilizes a linear test-statistic, enabling the computation of closed form p-value bounds, as well as a standard asymptotic normality result. OASIS provides a partitioning of the table for rejected hypotheses, lending interpretability to its rejection of the null. In genomic applications, OASIS performs reference-free and metadata-free variant detection in SARS-CoV-2 and M. Tuberculosis, and demonstrates robust performance for single cell RNA-sequencing, all tasks without existing solutions.
Integrative proteomics and transcriptomics of human T-cells reveals temporal metabolic reprogramming following TCR-induced activation

T-cells are critical components of the adaptive immune system. Upon activation, they acquire effector functions through a complex interplay between mRNA transcripts and proteins, the landscape of which remains to be fully elucidated. In this resource article, we present an integrative temporal proteomic and transcriptomic analysis of primary human CD4+ and CD8+ T-cells following ex vivo activation with anti-CD3/CD28 Dynabeads. Our data reveal a time-dependent dissociation between the T-cell transcriptome and proteome during activation. A transient downregulation of GLUT1, the central glucose transporter in T-cells, marked the onset of reprogramming in both CD4+ and CD8+ T-cells. At late activation, CD4+ T-cells upregulated enzymes associated with degradation of fatty acids while CD8+ T-cells preferentially upregulated enzymes in the metabolism of cofactors and vitamins. Surprisingly, we found that activated CD4+ and CD8+ T-cells became transcriptionally more divergent at the same time their proteome became more similar. In addition to the metabolic reprogramming highlighted in our analysis, this dataset provides a public resource for understanding temporal molecular changes governing the acquisition of effector functions by T-cells.
Repurposing the dark genome. II - Reverse Proteins

Based on the expression blueprint encoded in the genome, three groups of sequences have been identified – protein encoding, RNA encoding, and non-expressing. We asked: Why did nature choose a particular DNA sequence for expression? Did she sample every possibility, approving some for RNA synthesis, some for protein synthesis, and retiring/ignoring the rest. If evolution randomly selected sequences for metabolic trials, how much non-utilized (not-expressing) and under-utilized (only RNA encoding) information is currently available for innovations? These questions lead us to experimentally synthesizing functional proteins from intergenic sequences of E.coli (Dhar et al 2009). The current work is an extension of this original report and takes into consideration natural protein-coding sequences ‘read backward’ to generate a new possibility. Reverse proteins are full-length ‘translation equivalents’ of the existing protein-coding genes read in the -1 frame. The structural, functional and interaction predictions of reverse proteins in E.coli, S.cerevisiae and D.melanogaster, open up a new opportunity of producing ‘first-in-the-class’ proteins towards functional endpoints. This study points to a large untapped genomic space from the fundamental biology and applications perspectives.