Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk factors for infectiousness of patients with tuberculosis: a systematic review and meta-analysis

Abstract We performed a systematic review and meta-analyses of studies assessing tuberculosis (TB) patient-related risk factors for transmission of Mycobacterium tuberculosis infection. Meta-analyses were conducted for sputum smear-positivity, lung cavitation and HIV seropositivity of index patients with both crude and adjusted odds ratios (AORs) pooled using random effect models. Thirty-seven studies were included in the review. We found that demographic characteristics such as age and sex were not significant risk factors, while behaviours such as smoking and alcohol intake were associated with infectiousness although inconsistently. Treatment delay of >28 days was a significant predictor of greater infectiousness. Contacts of sputum smear-positive index patients were found to be more likely to be infected than contacts of sputum smear-negative patients, with a pooled AOR of 2.15 (95% confidence interval (CI) 1.47–3.17, I2 = 38%). Similarly, contacts of patients with the cavitary disease were around twice as likely to be infected as contacts of patients without cavitation (pooled AOR 1.9, 95% CI 1.26–2.84, I2 = 63%). In contrast, HIV seropositive patients were associated with few contact infections than HIV seronegative patients (AOR 0.45, 95% CI 0.26–0.80, I2 = 52%). In conclusion, behavioural and clinical characteristics of TB patients can be used to identify highly infectious patients for targeted interventions.
Semiparametric regression analysis for alternating recurrent event data

Alternating recurrent event data arise frequently in clinical and epidemiologic studies, where 2 types of events such as hospital admission and discharge occur alternately over time. The 2 alternating states defined by these recurrent events could each carry important and distinct information about a patient's underlying health condition and/or the quality of care. In this paper, we propose a semiparametric method for evaluating covariate effects on the 2 alternating states jointly. The proposed methodology accounts for the dependence among the alternating states as well as the heterogeneity across patients via a frailty with unspecified distribution. Moreover, the estimation procedure, which is based on smooth estimating equations, not only properly addresses challenges such as induced dependent censoring and intercept sampling bias commonly confronted in serial event gap time data but also is more computationally tractable than the existing rank‐based methods. The proposed methods are evaluated by simulation studies and illustrated by analyzing psychiatric contacts from the South Verona Psychiatric Case Register.
Prostacyclin Enhances the Expression of LPS/INF-γ-Induced Nitric Oxide Synthase in Human Monocytes

Background: Nitric oxide (NO) is an important mediator of inflammatory processes, including macrophage-mediated cellular host defense, and is found to be increased in peritonitis. The ability of human mononuclear cells to contribute to the NO production by expression of active inducible NO synthase (iNOS) is still discussed controversely. Aims: This study was designed to investigate the influence of prostacyclin receptor (IP receptor) activation on iNOS expression and NO formation in human peripheral blood monocytes. Method and Results: Using reverse transcriptase-polymerase chain reaction, we demonstrated that human monocytes express high levels of IP receptor mRNA. Stimulation of monocytes with the IP receptor selective agonist cicaprost (100 nM) significantly induced cellular cyclic adenosine monophosphate formation, indicating functional coupling of the receptor to Gs. Treatment of cells with lipopolysaccharide (LPS)/interferon gamma (IFN-γ) further enhanced the IP receptor mRNA expression 2.7 ± 0.1-fold above basal levels (n = 6). Analysis of iNOS expression revealed barely detectable mRNA levels in unstimulated monocytes which were increased 3.75 ± 0.3-fold (n = 5) after costimulation with 1 µg/ml LPS and 250 U/ml INF-γ for 16 h. Further increases of iNOS mRNA expression (9.4 ± 0.9-fold above basal, n = 5) were obtained, if the monocytes were costimulated with 1 µg/ml LPS, 250 U/ml INF-γ, and 100 nM cicaprost for 16 h. Measurement of the NO generation correlated with the polymerase chain reaction data: treatment of cells with 1 µg/ml LPS plus 250 U/ml INF-γ increased the NO2 production to 2.6 µM, being above the basal level of 2.0 µM, as determined in the cell culture medium. Additional treatment with 100 nM cicaprost further significantly increased the NO2 production to 3.43 µM. Conclusions: An IP receptor mediated increase in cyclic adenosine monophosphate formation plays an important role in enhancing LPS/IFN-γ-induced iNOS expression in human monocytes/macrophages and may, therefore, contribute to the increased production of NO during peritonitis.
Correctness assessment of a crowdcoding project in a computer programming introductory course

Crowdcoding is a programming model that outsources a software project implementation to the crowd. As educators, we think that crowdcoding could be leveraged as part of the learning path of engineering students from a computer programming introductory course to solve local community problems. The benefits are twofold: on the one hand the students practice the concepts learned in class and, on the other hand, they participate in real‐life problems. Nevertheless, several challenges arise when developing a crowdcoding platform, the first one being how to check the correctness of student's code without giving an extra burden to the professors in the course. To overcome this issue, we propose a novel system that does not resort to expert review; neither requires knowing the right answers beforehand. The proposed scheme automatically clusters the student's codes based solely on the output they produce. Our initial results show that the largest cluster contains the same codes selected as correct by the automated and human testing, as long as some conditions apply.
Task‐Sharing Approaches to Improve Mental Health Care in Rural and Other Low‐Resource Settings: A Systematic Review

PURPOSE Rural areas persistently face a shortage of mental health specialists. Task shifting, or task sharing, is an approach in global mental health that may help address unmet mental health needs in rural and other low-resource areas. This review focuses on task-shifting approaches and highlights future directions for research in this area. METHODS Systematic review on task sharing of mental health care in rural areas of high-income countries included: (1) PubMed, (2) gray literature for innovations not yet published in peer-reviewed journals, and (3) outreach to experts for additional articles. We included English language articles published before August 31, 2013, on interventions sharing mental health care tasks across a team in rural settings. We excluded literature: (1) from low- and middle-income countries, (2) involving direct transfer of care to another provider, and (3) describing clinical guidelines and shared decision-making tools. FINDINGS The review identified approaches to task sharing focused mainly on community health workers and primary care providers. Technology was identified as a way to leverage mental health specialists to support care across settings both within primary care and out in the community. The review also highlighted how provider education, supervision, and partnerships with local communities can support task sharing. Challenges, such as confidentiality, are often not addressed in the literature. CONCLUSIONS Approaches to task sharing may improve reach and effectiveness of mental health care in rural and other low-resource settings, though important questions remain. We recommend promising research directions to address these questions.
Paralinguistic Variation and Invariance in the Characteristic Frequencies of Vowels

Abstract It is shown that within-speaker variations in vocal effort and phonation affect fundamental frequency (F₀) and the formant frequencies of vowels in the sense of a linear compression/expansion of the spectral separations between them, given an adequate scaling of pitch. Between-speaker variations in size correspond to a translation of the spectral peaks shaped by F₀ and the formants if pitch is scaled tonotopically (in Bark). On the basis of these observations, invariant cues to vowel quality are suggested. It is further shown that vowels produced by adult women tend to be phonetically more explicit and, hence, more peripheral in ‘vowel space’ than those of men and children. It is also shown that the formant frequencies of vowels subjected to paralinguistic variation are related by power functions of frequency.
Hiding Feelings for Whose Sake? Attachment Avoidance, Relationship Connectedness, and Protective Buffering Intentions

Why do some people refrain from disclosing distress, even to those they feel closest to? Protective buffering, a coping strategy that involves hiding worries from one’s partner, may carry mental health costs for those enacting it and the target of their protection. Although the strategy is often assumed to be targeted at a partner to shield him or her from distress (i.e., used with partner-protective intentions), it can also be used for one’s own benefit (i.e., with self-protective intentions). Guided by attachment theory, the current research identified dispositional and relational factors that may explain and predict when people use the strategy to what end. In addition, this research tested whether self-protective and partner-protective intentions are associated with distinct outcomes for mental health. Study 1 showed that highly avoidant individuals deem it wrong to burden their partner with distress expressions and that such beliefs increase with greater dependence on the relationship. Accordingly, across 3 studies (Studies 2–4), highly avoidant individuals reported using protective buffering to spare their partner when feeling strongly connected to him or her. However, when feeling less connected, highly avoidant individuals used protective buffering to minimize their own distress. Moreover, individuals who intended to self-protect reported more depressive symptoms (Study 3), and at the dyadic level, individuals also reported more mental health symptoms when their partner had greater self-protective intentions (Study 4). By contrast, partner-protective intentions (individuals’ own or their partners’) were unrelated to mental health. Theoretical and applied implications and future directions are discussed.
Finding Optimal Team for Multiskill Task Based on Vehicle Sensors Data

These days, with the increasingly widespread employment of sensors, particularly those attached to vehicles, the collection of spatial data is becoming easier and more accurate. As a result, many relevant areas, such as spatial crowdsourcing, are gaining ever more attention. A typical spatial crowdsourcing scenario involves an employer publishing a task and some workers helping to accomplish it. However, most of previous studies have only considered the spatial information of workers and tasks, while ignoring individual variations among workers. In this paper, we consider the Software Development Team Formation (SDTF) problem, which aims to assemble a team of workers whose abilities satisfy the requirements of the task. After showing that the problem is NP-hard, we propose three greedy algorithms and a multiple-phase algorithm to approximately solve the problem. Extensive experiments are conducted on synthetic and real datasets, and the results verify the effectiveness and efficiency of our algorithms.
New Approach to Categorical Semantics for Procedural Languages

The semantics of programs written in some languages is concerned with the interpretation in various types of models. The purpose of structural operational semantics is to describe how a computation is performed. This method is one of the most popular semantic methods in the community of software engineers. It describes program behavior in the form of state changes caused by the execution of elementary steps. This feature predestinates the usage of the structural operational semantics for implementation of programming languages and also for verification purposes. Another semantic method, denotational semantics, defines changes of states by functions. In this paper a new approach to semantics is presented: behavior of programs, i.e., changes of states are modeled in the category of states. The morphisms category expresses elementary execution steps and the program execution is an oriented path in the category, i.e. composition of morphisms. Our categorical model is constructed for a simple procedural language that contains all basic van Dijkstra's constructs. We enriched our approach also with procedures forming a collection of categories interconnected by functors. This method enables the repeated call of procedures, nesting of procedure calls and recursive calls. Moreover, it allows to illustrate and accentuate dynamics of the program execution. The simplicity of this method does not exclude its mathematical exactness.
SAM-VI RNAs selectively bind S-adenosylmethionine and exhibit similarities to SAM-III riboswitches

ABSTRACT Five distinct riboswitch classes that regulate gene expression in response to the cofactor S-adenosylmethionine (SAM) or its metabolic breakdown product S-adenosylhomocysteine (SAH) have been reported previously. Collectively, these SAM- or SAH-sensing RNAs constitute the most abundant collection of riboswitches, and are found in nearly every major bacterial lineage. Here, we report a potential sixth member of this pervasive riboswitch family, called SAM-VI, which is predominantly found in Bifidobacterium species. SAM-VI aptamers selectively bind the cofactor SAM and strongly discriminate against SAH. The consensus sequence and structural model for SAM-VI share some features with the consensus model for the SAM-III riboswitch class, whose members are mainly found in lactic acid bacteria. However, there are sufficient differences between the two classes such that current bioinformatics methods separately cluster representatives of the two motifs. These findings highlight the abundance of RNA structures that can form to selectively recognize SAM, and showcase the ability of RNA to utilize diverse strategies to perform similar biological functions.
Stroke Case Fatality in Denmark from 1977 to 1992: The Copenhagen City Heart Study

Background and Purpose: Stroke mortality rates have decreased in Denmark but little is known about the reasons for these changes. One possible explanation is decreased case-fatality, and the aim of the present investigation was to study trends in case-fatality for first-ever stroke in a large population-based cohort study in Copenhagen, Denmark. Subjects and Methods: The Copenhagen City Heart Study comprised 19,698 inhabitants in Copenhagen, Denmark. Linkage to two national registers enabled identification of all subjects irrespective of participation in the study examinations. Follow-up in the present study was from January 1, 1977 to December 31, 1992. Case fatality after 7 days, 28 days, 1 year and 1 year in 28-day survivors was assessed for first-ever stroke. Uniform identification and validation methods made it possible to estimate trends in case-fatality. The World Health Organization’s definition of stroke was used, and stroke was categorized into either unspecified stroke, ischemic infarction, intracerebral hemorrhage, or subarachnoid hemorrhage. The effect of time was estimated by means of multiple logistic regression analyses adjusting for gender, age at onset and type of stroke. Results: A total of 1,213 strokes occurred during the study period from 1977 to 1992 in the study population. The case-fatality was highest during the first 28 days, and especially the initial 7 days; thereafter a steady state was reached. From the period 1977–1980 to the period 1989–1992 case-fatality did not change in analyses of 7-day case-fatality odds ratio (OR) = 1.14 (95% confidence interval, CI: 0.98–1.33), or of 28-day case-fatality OR = 1.06 (95% CI: 0.92–1.20), or of 1-year case-fatality OR = 0.95 (95% CI: 0.84–1.07). In the 1-year case-fatality, including only 28-day survivors, a significant decrease was found OR = 0.81 (95% CI: 0.67–0.97). Men had a significantly lower 7-day case-fatality than women; OR = 0.73 (95% CI: 0.52–0.99), but the difference attenuated in subsequent analyses and did not remain statistically significant. Conclusion: During the period 1977–1992, the 1-year case-fatality decreased in stroke patients who survived the initial 28 days, whereas no changes were observed in 7-day, 28-day and 1-year case-fatality.
Translational Implications of Platelets as Vascular First Responders

Platelets play a vital role in normal hemostasis to stem blood loss at sites of vascular injury by tethering and adhering to sites of injury, recruiting other platelets and blood cells to the developing clot, releasing vasoactive small molecules and proteins, and assembling and activating plasma coagulation proteins in a tightly regulated temporal and spatial manner. In synchrony with specific end products of coagulation, primarily cross-linked fibrin, a stable thrombus quickly forms. Far beyond physiological hemostasis and pathological thrombosis, emerging evidence supports platelets playing a pivotal role in vascular homeostasis, inflammation, cellular repair, regeneration, and wide range of autocrine and paracrine functions. In essence, platelets play both structural and functional roles as reporters, messengers, and active transporters surveying the vasculature for cues of environmental or developmental stimuli and participating as first responders.1 In this review, we will provide a contemporary perspective of platelet physiology, including fundamental, translational, and clinical constructs that apply directly to human health and disease.
Multimodal speech recognition using mouth images from depth camera

Deep learning has been proved to be effective in multimodal speech recognition using facial frontal images. In this paper, we propose a new deep learning method, a trimodal deep autoencoder, which uses not only audio signals and face images, but also depth images of faces, as the inputs. We collected continuous speech data from 20 speakers with Kinect 2.0 and used them for our evaluation. The experimental results with 10dB SNR showed that our method reduced errors by 30%, from 34.6% to 24.2% from audio-only speech recognition when SNR was 10dB. In particular, it is effective for recognizing some consonants including /k/, /t/.
Operationalizing wait lists: Strategies and experiences in three hospital outpatient physiotherapy departments in Montreal

ABSTRACT In Canada, limited resources and increasing demand place pressure on the public healthcare system, something that is likely to increase. In this context, wait lists in outpatient physiotherapy departments (OPD) will get longer, system inefficiencies will arise, and frustrations and ethical concerns will be experienced by patients and staff. To better understand the perceptions of OPD staff regarding priority setting, treatment frequency, treatment duration, and wait list management strategies, we conducted an Interpretive Description study involving semi-structured interviews in three OPDs in Montreal. Participants discussed factors that influenced their decision making about who was prioritized to receive care, strategies that were used to respond to an imbalance between needs and resources in the OPDs and procedures to manage wait lists to help improve access to care. While clinical needs are central in approaches to prioritization, other non-clinical factors relating to the patient, the physiotherapist, and the institution also influence decisions. We examine these findings through the lens of complexity theory, providing insight into opportunities and obstacles for the implementation of management strategies in OPDs. These strategies will need to be carefully evaluated in order to create evidence-based guidelines for wait list management in other settings.
Inhibition of neutrophil elastase-induced interleukin-8 gene expression by urinary trypsin inhibitor in human bronchial epithelial cells.

BACKGROUND Urinary trypsin inhibitor (UTI), a potential inhibitor for proteinases including neutrophil elastase (NE), trypsin, plasmin, cathepsin B and H has been used for the treatment of lung diseases with the absence of side effects in Japan. METHODS In this study, we investigated the inhibitory effects of UTI on both purified NE and NE activities present in bronchoalveolar fluids from patients with chronic bronchitis. We also investigated the inhibitory capacity of UTI with regard to NE-induced interleukin-8 gene expression in human bronchial epithelial cells by Northern analyses. RESULTS UTI inhibited NE activities in bronchoalveolar lavage fluid from patients with chronic bronchitis and of the purified enzyme. In addition, UTI inhibited NE-induced interleukin-8 gene expression and protein secretion in a human bronchial epithelial cell line. CONCLUSIONS Our results suggest that UTI is applicable to patients with a variety inflammatory lung diseases in which NE plays a pivotal role.
Comparison of the Amplitude/Intensity Function of the Auditory Evoked N1m and N1 Components

This study compared the intensity dependence of the auditory evoked N1 and N1m components in 10 healthy subjects. The evoked responses were recorded simultaneously at 33 channels for the auditory evoked potentials (AEP) and with a 37-channel magnetometer for the auditory evoked fields (AEF). They were satisfactorily modeled by a tangential and a radial dipole per hemisphere for the N1 component and a tangential dipole in the left hemisphere for the N1m component. The tangential dipoles showed different dipole characteristics. The amplitude of the AEP rose significantly with increasing stimulus intensity whereas the amplitudes of the AEF tended to plateau between the highest intensities. The magnetic dipole shifted to the surface of the skull with higher stimulus intensity whereas the electric tangential dipole moved to the center of the skull. The latencies decreased with increasing stimulus intensity.
Downregulated apoptosis and autophagy after anti‐Aβ immunotherapy in Alzheimer's disease

Aβ immunization of Alzheimer's disease (AD) patients in the AN1792 (Elan Pharmaceuticals) trial caused Aβ removal and a decreased density of neurons in the cerebral cortex. As preservation of neurons may be a critical determinant of outcome after Aβ immunization, we have assessed the impact of previous Aβ immunization on the expression of a range of apoptotic proteins in post‐mortem human brain tissue. Cortex from 13 AD patients immunized with AN1792 (iAD) and from 27 nonimmunized AD (cAD) cases was immunolabeled for proapoptotic proteins implicated in AD pathophysiology: phosphorylated c‐Jun N‐terminal kinase (pJNK), activated caspase3 (a‐casp3), phosphorylated GSK3β on tyrosine 216 (GSK3βtyr216), p53 and Cdk5/p35. Expression of these proteins was analyzed in relation to immunization status and other clinical data. The antigen load of all of these proapoptotic proteins was significantly lower in iAD than cAD (P < 0.0001). In cAD, significant correlations (P < 0.001) were observed between: Cdk5/p35 and GSK3βtyr216; a‐casp3 and Aβ42; p53 and age at death. In iAD, significant correlations were found between GSK3βtyr216 and a‐casp3; both spongiosis and neuritic curvature ratio and Aβ42; and Cdk5/p35 and Aβ‐antibody level. Although neuronal loss was increased by immunization with AN1792, our present findings suggest downregulation of apoptosis in residual neurons and other cells.