Miracle-dz/UniFAR-FTUs huggingface dataset:
Pembrolizumab induces HIV latency reversal in people living with HIV and cancer on antiretroviral therapy

In people living with HIV (PLWH) on antiretroviral therapy (ART), virus persists in a latent form where there is minimal transcription or protein expression. Latently infected cells are a major barrier to curing HIV. Increasing HIV transcription and viral production in latently infected cells could facilitate immune recognition and reduce the pool of infected cells that persist on ART. Given that programmed cell death protein 1 (PD-1) expressing CD4+ T cells are preferentially infected with HIV in PLWH on ART, we aimed to determine whether administration of antibodies targeting PD-1 would reverse HIV latency in vivo. We therefore evaluated the impact of intravenous administration of pembrolizumab every 3 weeks on HIV latency in 32 PLWH and cancer on ART. After the first infusion of anti–PD-1, we observed a median 1.32-fold increase in unspliced HIV RNA and 1.61-fold increase in unspliced RNA:DNA ratio in sorted blood CD4+ T cells compared to baseline. We also observed a 1.65-fold increase in plasma HIV RNA. The frequency of CD4+ T cells with inducible virus evaluated using the tat/rev limiting dilution assay was higher after 6 cycles compared to baseline. Phylogenetic analyses of HIV env sequences in a participant who developed low concentrations of HIV viremia after 6 cycles of pembrolizumab did not demonstrate clonal expansion of HIV-infected cells. These data are consistent with anti–PD-1 being able to reverse HIV latency in vivo and support the rationale for combining anti–PD-1 with other interventions to reduce the HIV reservoir. Description Monoclonal antibodies targeting PD-1 potentiate HIV transcription in CD4+ T cells in humans with HIV and advanced cancer on antiretroviral therapy. PD-1 blockade for HIV Strategies to target and reverse the latent HIV reservoir are required to cure HIV. Because CD4+ T cells expressing programmed cell death protein 1 (PD-1) are preferentially infected with HIV in an individual on antiretroviral therapy, PD-1 is an attractive target to manipulate the latent reservoir. To this end, Uldrick et al. measured the impact of anti–PD-1 treatment with pembrolizumab on the HIV reservoir in 32 individuals living with HIV on suppressive antiretroviral therapy and diagnosed with cancer. They observed evidence of increased unspliced HIV RNA and of the unspliced RNA:DNA ratio, consistent with anti–PD-1 treatment having the potential to reverse HIV latency. Further studies are needed to evaluate the dose and frequency of anti–PD-1 treatment required for latency reversal.
Cohort Profile: The United Kingdom Research study into Ethnicity and COVID-19 outcomes in Healthcare workers (UK-REACH)

Key Features of the UK-REACH Cohort (Profile in a nutshell) The UK-REACH Cohort was established to understand why ethnic minority healthcare workers (HCWs) are at risk of poorer outcomes from COVID-19 when compared to their white ethnic counterparts in the United Kingdom (UK). Through study design, it contains a uniquely high percentage of participants from ethnic minority backgrounds about whom a wide range of qualitative and quantitative data has been collected. A total of 17891 HCWs aged 16-89 years (mean age: 44) have been recruited from across the UK via all major healthcare regulators, individual National Health Service (NHS) hospital trusts and UK HCW membership bodies who advertised the study to their registrants/staff to encourage participation in the study. Data available include linked healthcare records for 25 years from the date of consent and consent to obtain genomic sequencing data collected via saliva. Online questionnaires include information on demographics, COVID-19 exposures at work and home, redeployment in the workforce due to COVID-19, mental health measures, workforce attrition, and opinions on COVID-19 vaccines, with baseline (n=15 119), 6 (n=5632) and 12-month follow-up data captured. Request data access and collaborations by following documentation found at https://www.uk-reach.org/main/data_sharing.
Nucleocapsid Antigenemia Is a Marker of Acute SARS-CoV-2 Infection

Reliable detection of SARS-CoV-2 infection is essential for diagnosis and treatment of disease as well as infection control and prevention during the ongoing COVID-19 pandemic. Existing nucleic acid tests do not reliably distinguish acute from resolved infection, as residual RNA is frequently detected in the absence of replication-competent virus. We hypothesized that viral nucleocapsid in serum or plasma may be a specific biomarker of acute infection that could enhance isolation and treatment strategies at an individualized level. Samples were obtained from a retrospective serological survey using a convenience sampling method from adult inpatient and outpatient encounters from January through March 2021. Samples were categorized along a timeline of infection (e.g. acute, late presenting, convalescent) based on timing of available SARS-CoV-2 testing and symptomatology. Nucleocapsid was quantified by digital immunoassay on the Quanterix HD-X platform. In a large sample of 1860 specimens from 1607 patients, the highest level and frequency of antigenemia were observed in samples obtained during acute SARS-CoV-2 infection. Levels of antigenemia were highest in samples from seronegative individuals and in those with more severe disease. Using ROC analysis, we found that antigenemia exhibited up to 85.8% sensitivity and 98.6% specificity as a biomarker for acute COVID-19. Nucleocapsid antigenemia is a sensitive and specific biomarker for acute SARS-CoV-2 infection and may aid in individualized assessment of SARS-CoV-2 infection resolution or persistence, although interpretation is limited by absence of a diagnostic gold standard for active infection.
Viral Cultures for Assessing Fomites Transmission of SARS-CoV-2: a Systematic Review Protocol

This is a protocol for a systematic review to assess fomite transmission in SARS-CoV-2. Our research questions are as follows: 1. Are fomite samples infectious? 2 If so, what proportion are infectious, and what is the distance and duration of infectiousness in the air? 3. What is the relationship between fomites, infectiousness and PCR cycle threshold (Ct)? 4. Is there evidence of a chain of transmission that establishes an actual instance of fomite transmission of SARS-CoV-2? We will include studies of any design (and in any setting) that investigate fomite transmission (defined as any inanimate object that, when contaminated with or exposed to infectious agents, can transfer the agent to a new host). We will only include studies that performed viral culture which assessed cytopathic effect and verification techniques to ensure the cultured virus is SARS-CoV-2. We will assess the risk of bias using a checklist modified from the QUADAS-2 criteria.
Diagnostic accuracy of chest X-ray interpretation for tuberculosis by three artificial intelligence-based software in a screening use-case: an individual patient meta-analysis of global data

Background Chest X-ray (CXR) screening is a useful diagnostic tool to test individuals at high risk of tuberculosis (TB), yet image interpretation requires trained human readers who are in short supply in many high TB burden countries. Therefore, CXR interpretation by computer-aided detection software (CAD) may overcome some of these challenges, but evidence on its accuracy is still limited. We established a CXR library with images and metadata from individuals and risk groups that underwent TB screening in a variety of countries to assess the diagnostic accuracy of three commercial CAD solutions through an individual participant meta-analysis. Methods and findings We collected digital CXRs and demographic and clinical data from 6 source studies involving a total of 2756 participants, 1753 (64%) of whom also had microbiological test information. All CXR images were analyzed with CAD4TB v6 (Delft Imaging), Lunit Insight CXR TB algorithm v4.9. 0 (Lunit Inc.), and qXR v2 (Qure.ai) and re-read by an expert radiologist who was blinded to the initial CXR reading, the CAD scores, and participant information. While the performance of CAD varied across source studies, the pooled, meta-analyzed summary receiver operating characteristic (ROC) curves of the three products against a microbiological reference standard were similar, with area under the curves (AUCs) of 76.4 (95% CI 72.1-80.3) for CAD4TB, 83.3 (95% CI 78.4-87.2) for Lunit, and 76.4 (95% CI 72.1-80.3) for qXR. None of the CAD products, or the radiologists, met the targets for a triage test of 90% sensitivity and 70% specificity. At the same sensitivity of the expert radiologist (94.0%), all CAD had slightly lower point estimates for specificity (22.4% (95% CI 16.9-29.0) for CAD4TB, 34.6% (95% CI 25.3-45.1) for qXR, and 41.0% (95% CI 30.1-53.0) for Lunit compared to 45.6% for the expert radiologist). At the same specificity of 45.6%, all CAD products had lower point estimates for sensitivity but overlapping CIs with the sensitivity estimate of the radiologist. Conclusions We showed that, overall, three commercially available CAD products had a reasonable diagnostic accuracy for microbiologically confirmed pulmonary TB and may achieve a sensitivity and specificity that approximates those of experienced radiologists. While threshold setting and cost-effectiveness modelling are needed to inform the optimal implementation of CAD products as part of screening programs, the availability of CAD will assist in scaling up active case finding for TB and hence contribute to TB elimination in these settings.
Decreased Diversity and Abundance of Marine Invertebrates at CO2 Seeps in Warm-Temperate Japan

Japan has many coastal carbon dioxide seeps as it is one of the most volcanically active parts of the world. These shallow seeps do not have the spectacular aggregations of specialist fauna seen in deep-sea vent systems but they do have gradients in seawater carbonate chemistry that are useful as natural analogues of the effects of ocean acidification on marine biodiversity, ecosystem function and fisheries. Here, we compare macroinvertebrate diversity and abundance on rocky habitats at ambient (mean ≤ 410 µatm) and high (mean 971–1484 µatm) levels of seawater pCO2 in the warm-temperate region of Japan, avoiding areas with toxic sulphur or warm-water conditions. We show that although 70% of intertidal taxa and 40% of shallow subtidal taxa were able to tolerate the high CO2 conditions, there was a marked reduction in the abundance of corals, bivalves and gastropods in acidified conditions. A narrower range of filter feeders, grazers, detritivores, scavengers and carnivores were present at high CO2 resulting in a simplified coastal system that was unable to retain the high standing stocks of marine carbon biomass found in ambient conditions. It is clear that cuts in CO2 emissions would reduce the risks of climate change and ocean acidification impacts on marine biodiversity, shellfish production and biomass in the rocky coastal shores of this region.
Still Learning from Gregor Mendel after 200 Years

Abstract Although unrecognized for his scientific achievements during his life, Gregor Mendel pioneered our modern understanding of the gene, work that shaped the field of genetics and advances in biology and medicine. The field that he set in motion 200 years ago lies at the center of current ethical debates about the future of humanity, the limits of science, and how best to employ our knowledge for betterment of the human condition. Mendel's personal life also offers lessons, especially for those of us engaged in teaching future generations.
Using third-party evaluations to assess socioemotional skills in graduate and professional school admissions

Abstract Consideration of socioemotional skills in admissions potentially can increase representation of racial and ethnic minorities and women in graduate and professional education as well as identify candidates more likely to succeed in graduate and professional school. Research on one such assessment, the ETS Personal Potential Index (PPI), showed that the PPI produced much smaller racial/ethnic-gender group mean score differences than undergraduate grade point average (UGPA) and the Graduate Record Examinations (GRE) did. Across levels of institutional selectivity, the PPI can promote racial/ethnic and gender diversity in graduate and professional school in ways that UGPA and GRE scores do not. Predictive validity analyses showed that for doctoral STEM programs the PPI dimensions of (1) Planning and Organization and (2) Communication Skills positively predict school grade point average as well as a lower risk of academic probation, a determinant of degree progress, both alone and incrementally over UGPA and GRE scores. Supplemental data for this article is available online at https://doi.org/10.1080/15305058.2021. 2019748 .
Temple, Huygens and ‘sharawadgi’: tempering the passions to achieve tranquillity

Among us, the Beauty of Building and Planting is placed chiefly, in some certain Proportions, Symmetries, or Uniformities; our Walks and our Trees ranged so, as to answer one another, and at exact Distances. The Chineses scorn this way of Planting, and say a Boy that can tell an hundred, may plant Walks of Trees in strait Lines, and over against one another, and to what Length and Extent He pleases. But their greatest reach of Imagination, is employed in contriving Figures, where the Beauty shall be great, and strike the eye, but without any order or disposition of parts, that shall be commonly or easily observ’d. And though we have hardly any Notion of this sort of Beauty, yet they have a particular Word to express it; and where they find it hit their Eye at first sight, they say the Sharawadgi is fine or is admirable, or any such expression of Esteem.
Perinatal mortality audits and reporting of perinatal deaths: systematic review of outcomes and barriers

Abstract Background Perinatal deaths are a devastating experience for all families and healthcare professionals involved. Audit of perinatal mortality (PNM) is essential to better understand the factors associated with perinatal death, to identify key deficiencies in healthcare provision and should be utilised to improve the quality of perinatal care. However, barriers exist to successful audit implementation and few countries have implemented national perinatal audit programs. Content We searched the PubMed, EMBASE and EBSCO host, including Medline, Academic Search Complete and CINAHL Plus databases for articles that were published from 1st January 2000. Articles evaluating perinatal mortality audits or audit implementation, identifying risk or care factors of perinatal mortality through audits, in middle and/or high-income countries were considered for inclusion in this review. Twenty articles met inclusion criteria. Incomplete datasets, nonstandard audit methods and classifications, and inadequate staff training were highlighted as barriers to PNM reporting and audit implementation. Failure in timely detection and management of antenatal maternal and fetal conditions and late presentation or failure to escalate care were the most common substandard care factors identified through audit. Overall, recommendations for perinatal audit focused on standardised audit tools and training of staff. Overall, the implementation of audit recommendations remains unclear. Summary This review highlights barriers to audit practices and emphasises the need for adequately trained staff to participate in regular audit that is standardised and thorough. To achieve the goal of reducing PNM, it is crucial that the audit cycle is completed with continuous re-evaluation of recommended changes.
The effects of COVID-19 on employment, labor markets, and gender equality in Central America

Abstract This study considers the economic impact of coronavirus disease 2019 (COVID-19) on commercial enterprises in four Central American countries – El Salvador, Guatemala, Honduras, and Nicaragua. At the time of analysis, neither the pandemic nor its economic consequences had fully run their course. It is not, therefore, a definitive analysis, but it is important to try to draw important lessons as soon as possible. The main focus of the study was the initial impact on labor markets. The analysis was based on World Bank Enterprise Surveys undertaken before the outbreak of COVID-19 and follow-up surveys on the effects of the pandemic, also undertaken by the World Bank (Source: Enterprise Surveys, The World Bank, http://www.enterprisesurveys.org). These were combined with data on both government containment measures and rates of morbidity and mortality. The use of enterprise data to analyze labor market issues has some limitations but also many strengths. The data are useful for analyzing the consequences for gender equality in employment. Since the demand for labor is a derived demand, firm-level data provide a clear link to labor market effects. The pandemic has caused a significant loss in sales for many firms. This has created a loss of liquidity, which, in turn, has caused some firms to reduce employment, working hours, and wages. Government containment measures necessary to save lives, such as temporary workplace closures, have added to the burden for both firms and employees. The study starts by using the surveys to identify the important stylized facts. Although some issues are already well documented anecdotally through media reports, this method provides a more evidence-based approach. It also helps identify several issues, such as the impact on gender equality, which has received less journalistic attention. The study is further supported by a regression analysis (ordinary least squares and seemingly unrelated regression equations models) of several key outcomes (changes in sales, employment, the share of females in employment, and expectations of firm survival). A limitation of such an analysis at any enterprise level is heterogeneity and, consequently, a risk of sample selection bias. To provide robustness checks, we use a matching approach. The results suggest that a significant proportion of surviving firms are vulnerable to permanent closure. The ability of firms to retain labor depends on sales, which are affected by both the pandemic itself and the government containment measures. Only a small proportion of firms have received government support, and there is evidence that it could help both firm survival and the retention of labor. There is some doubt whether the four countries have the institutional capacity to provide effective support. If such doubts prove well founded, then support may need to be externally driven.
Refining gentleness – a key to bulky CTMP

Abstract Chemithermomechanical pulp (CTMP) is often used in middle layers of multiply paperboards due to its high bulk at specified strength. Such a CTMP should consist of well-separated undamaged fibres with sufficient bonding capacity. The basic objective of this work is to examine the effect of refining on bulk, taking into account conditions such as temperature, sulphonation, refining gap and refiner size. First stage CTMP made from Norway spruce (Picea abies) were produced in pilot and mill scale trials. Two new parameters, Equivalent temperature related to softness and Refining gentleness are introduced that take into account refining conditions as actual temperature, softening temperature, bound sulphonate content, refining gap and refiner diameter. The results show that bulk increases linearly with refining gentleness.
Levels of communication: The talking horse experiments

Argument In the early twentieth century, counting and speaking horses, like the famous Clever Hans or the “Horses of Elberfeld,” became widely debated subjects in experimental psychology. The idea was to determine whether their learning success was only a fraud, or if it might open up a new chapter in “animal psychology” - or even belong to the realm of parapsychology and telepathy. When their tricks were discovered, the teachers of the animals were marked as charlatans. Both the attempts to detect charlatans and the efforts to avoid this accusation during the talking horse experiments proceeded using the method of introducing new levels of communication into the human-animal interaction process in order to substantiate each respective standpoint. This paper argues that the scientific studies and debates on the talking horses are relevant not only from psychological, biological, and semiotic vantage points, but also from the perspective of communications theory, giving rise to the foundational issue of levels of communication.
WAFL: Binary-Only WebAssembly Fuzzing with Fast Snapshots

WebAssembly, the open standard for binary code, is quickly gaining adoption on the web and beyond. As the binaries are often written in low-level languages, like C and C++, they are riddled with the same bugs as their traditional counterparts. Minimal tooling to uncover these bugs on WebAssembly binaries exists. In this paper we present WAFL, a fuzzer for WebAssembly binaries. WAFL adds a set of patches to the WAVM WebAssembly runtime to generate coverage data for the popular AFL++ fuzzer. Thanks to the underlying ahead-of-time (AOT) compiling WAVM, WAFL is already very performant. WAFL adds lightweight VM snapshots. By replacing forks, traditionally used in AFL++ harnesses, with WAFL’s snapshots, WAFL harnesses can even outperform native harnesses with compile-time instrumentation in raw fuzzing performance. To the best of our knowledge, WAFL is the first coverage-guided fuzzer for binary-only WebAssembly, without the need for source.
INVESTIGASI FAKTOR-FAKTOR YANG MEMPENGARUHI PARTISIPASI DISKUSI ONLINE: STUDI KASUS STUDENT-CENTERED E-LEARNING ENVIRONMENT MAGISTER TEKNOLOGI INFORMASI UNIVERSITAS INDONESIA

The use of e–Learning in Universitas Indonesia has been regulated by The Official Decree of The Rector of the Universitas Indonesia. Data derived from the log activity of SCeLE Admin shows that the discussion forum within SCeLE, from the year 2011 to 2014, has not been utilized optimally by both students and lecturers. This is shown by a number of discussion forums and topics that were below 15 percent. The objective of this research is to investigate the factors that influence participation of online discussions within SCeLE MTI Universitas Indonesia (UI). Data is collected using questionnaires that are given to 150 students of MTI Study Program UI. Data processing used partial least square–SEM (PLS-SEM) with the aid of smartPLS3 software. Research finding shows that several factors that influence SCeLE online discussion generally are extrinsic motivation, habit, information quality, performance expectancy, social influence, system quality, and service quality. The factors that are very influential to behavioral intention are performance expectancy, habit, extrinsic motivation and social influence. Meanwhile, the factors that are very influential to user satisfaction are information quality, system quality and service quality.