Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnosis of Human Echinococcosis via Exhaled Breath Analysis: A Promise for Rapid Diagnosis of Infectious Diseases Caused by Helminths

Background Human echinococcosis is a neglected infectious disease affecting more than 1 million people globally. Its diagnosis is expensive and difficult because of lack of adequate resources in low-resource locations, where most cases occur. Methods A group of volunteers diagnosed with the 2 main types of echinococcosis and corresponding control groups were recruited from hospitals in Tunisia (32 patients with cystic echinococcosis and 43 controls) and Poland (16 patients with alveolar echinococcosis and 8 controls). Breath samples were collected from all patients and analyzed by gas chromatography coupled to mass spectrometry, and a specifically developed electronic nose system. Results The chemical analysis revealed statistically different concentrations of 2 compounds in the breath of patients with cystic echinococcosis compared to controls, and statistically different concentrations of 7 compounds in the breath of patients with alveolar echinococcosis compared to controls. The discrimination accuracy achieved by the electronic nose system was 100% for cystic echinococcosis and 92.9% for alveolar echinococcosis, while the discrimination accuracy between these 2 patient groups was 92.1%. Conclusion Here we advocate a noninvasive, fast, easy-to-operate and nonexpensive diagnostic tool for the diagnosis of human echinococcosis disease through exhaled breath analysis, suitable for early diagnosis and population screening.
Determination of the Depth- and Time- Dependent Mechanical Behavior of Mouse Articular Cartilage Using Cyclic Reference Point Indentation

Mouse models of osteoarthritis and cartilage degeneration are important and powerful tools for investigating the molecular mechanisms of the disease pathology. Because of the vast number of genetically modified mouse models that are available for research, the ability to use these models is particularly attractive for the mechanobiologic interactions in the pathogenesis of osteoarthritis. However, the very small scale of mouse articular cartilage, where the healthy tissue is only 80 µm in thickness, poses challenges in quantifying mechanical characteristics of the tissue. We introduce here a novel approach that combines experimental and analytical methods to quantify the nuanced mechanical changes during cartilage degeneration at this scale. Cyclic reference point indentation is used to directly test the murine articular cartilage to obtain the force-deformation and the phase-shift characteristics of the tissue. The cartilage zonal thicknesses are confirmed from histology. These data are then fitted to a parallel spring model to determine the depth-dependent tissue stiffness and modulus. Using this approach, we investigated the effects of trypsin degradation on the zonal mechanical behavior of mouse articular cartilage. We observe a decline of the superficial zone stiffness coupled with the loss of the superficial layer. Subsequent degradation by trypsin allowed the identification of middle- and deep- zone properties. Taken together, this approach can be a useful tool for understanding the disease mechanisms of cartilage homeostasis and degeneration, and for monitoring of therapies for osteoarthritis.
Coil conversion to β‐strand induced by dimerization

Most molecular processes in living organisms rely on protein‐protein interactions, many of which are mediated by β‐sheet interfaces; this study investigates the formation of β‐sheet interfaces through the conversion of coils into β‐strands. Following an exhaustive search in the Protein Data Bank, the corresponding structural dimorphic fragments were extracted, characterized, and analyzed. Their short strand lengths and specific amino acid profiles indicate that dimorphic β‐strand interfaces are likely to be less stable than standard ones and could even convert to coil interfaces if their environment changes. Moreover, the construction of a simple classifier able to discriminate between the sequences of dimorphic and standard β‐strand interfaces suggests that the nature of those dimorphic sequences could be predicted, providing a novel means of identifying proteins capable of forming dimers.
A Web of Disheartenment With Hope on the Horizon: Intimate Partner Violence in Rural and Northern Communities

Intimate partner violence (IPV) has become a worldwide epidemic, yet little is known about the experiences of women survivors living in rural and Northern Canadian communities. Existing statistics suggest that women living in rural areas of the Canadian Prairie Provinces and Northwest Territories (NWT) are at a significantly higher risk of experiencing IPV. To better understand the experiences of IPV in these regions, qualitative interviews were conducted with service providers, including the Royal Canadian Mounted Police (RCMP), Victims Services, Shelter Services, counselors, and others (e.g., physicians). In total, 122 participants were interviewed. These interviews were analyzed using a grounded theory approach where the data/results were transformed into a pictorial matrix that documents the struggles that service providers endure. The matrix/results highlight how social issues, such as isolation and poverty, contribute to social oppressions, such as lack of resources, transportation, and/or services. As service providers struggle against these forces, they begin to develop feelings of disheartenment. Yet, they continue to fight because there are opposing forces, such as Emergency Intervention Orders, police transportation, and Victim Services, that demonstrate how societal response is improving the lives and increasing safety in rural and Northern communities. Ultimately, the results suggest that to reduce the incidences of IPV, we must go beyond the violent acts and deal with the social contexts in which IPV resides.
Readiness and recovery: Transferring between methadone and buprenorphine/naloxone for the treatment of opioid use disorder

Long-acting opioids are prescribed as part of treatment for opioid use disorders; methadone and buprenorphine are well researched and commonly prescribed for the treatment of opioid use disorder. Meta-analysis suggests that buprenorphine has a slightly poorer retention rate in treatment as compared to methadone. Benefits of buprenorphine/naloxone include greater ease in ceasing treatment and less use of illicit opioids while in treatment as compared to methadone. There are a number of qualitative and mixed-method studies that ask patients about their experiences of methadone maintenance and buprenorphine maintenance treatment. This research aimed to understand perspectives of receiving buprenorphine/naloxone for the treatment of opioid use disorder. A qualitative descriptive approach was used. Seven participants with a current diagnosis of opioid use disorder treated with buprenorphine/naloxone were interviewed. Thematic analysis extracted four themes: drivers for opioid substitution treatment change; readiness for buprenorphine/naloxone substitution treatment; absence of effect from buprenorphine/naloxone; and an increased sense of citizenship on buprenorphine/naloxone. This study identified a number of factors influencing participants' decision-making in transferring between methadone and buprenorphine/naloxone for the treatment of their opioid use disorder. Methadone was preferred by those seeking sedation and wishing to continue using other opioids, and buprenorphine/naloxone was most effective for participants no longer wishing to experience sedation and seeing opioid abstinence as an end point in their recovery. Changing treatment expectations are important to consider when determining medication selection and highlight the importance of quality information when determining the most suitable medication for the treatment of opioid use disorder.
Patient-ventilator asynchrony

ABSTRACT Patient-v entilator asynchrony (PVA) is a mismatch between the patient, regarding time, flow, volume, or pressure demands of the patient respiratory system, and the ventilator, which supplies such demands, during mechanical ventilation (MV). It is a common phenomenon, with incidence rates ranging from 10% to 85%. PVA might be due to factors related to the patient, to the ventilator, or both. The most common PVA types are those related to triggering, such as ineffective effort, auto-triggering, and double triggering; those related to premature or delayed cycling; and those related to insufficient or excessive flow. Each of these types can be detected by visual inspection of volume, flow, and pressure waveforms on the mechanical ventilator display. Specific ventilatory strategies can be used in combination with clinical management, such as controlling patient pain, anxiety, fever, etc. Deep sedation should be avoided whenever possible. PVA has been associated with unwanted outcomes, such as discomfort, dyspnea, worsening of pulmonary gas exchange, increased work of breathing, diaphragmatic injury, sleep impairment, and increased use of sedation or neuromuscular blockade, as well as increases in the duration of MV, weaning time, and mortality. Proportional assist ventilation and neurally adjusted ventilatory assist are modalities of partial ventilatory support that reduce PVA and have shown promise. This article reviews the literature on the types and causes of PVA, as well as the methods used in its evaluation, its potential implications in the recovery process of critically ill patients, and strategies for its resolution.
The association between body mass index, waist circumference, waist-hip ratio and cognitive disorder in older adults.

Purpose To examine the association between body mass index (BMI), waist circumference (WC), waist-hip ratio (WHR) and cognitive disorder in older adults. Methods Cross-sectional data from the mini-mental state examination questionnaire and physical examination of older adults (≥65, n = 1037) were collected and analyzed. Logistic regression examined the odds ratios (ORs) of cognitive performance according to BMI, WC and WHR. Results The prevalence of cognitive dysfunction in older adults was 13.0%. The BMI-based overweight rate, obesity rate and central obesity rate calculated by either WC or WHR were 39.6, 11.4% and 66.5, 65.6%, respectively. The risk of cognitive impairment was increased in elderly individuals ≥70 years old than in those <70 years old (OR = 1.738). In addition, gender, WHR and smoking habit were also significantly different between the two age groups (P < 0.05). We examined the effects of different BMI values and WC/WHR central obesity on cognition impairment in ≥70-year-old adults and found that BMI obesity and WC/WHR central obesity had a combined effect on the incidence of cognition impairment (OR = 3.076 and OR = 3.584). Conclusions BMI obesity and WC/WHR central obesity have a combined effect on cognitive impairment and WHR has a stronger association with cognitive impairment than WC.
Symptoms of persistent complex bereavement disorder, depression, and PTSD in a conjugally bereaved sample: a network analysis

Abstract Background Complicated and persistent grief reactions afflict approximately 10% of bereaved individuals and are associated with severe disruptions of functioning. These maladaptive patterns were defined in Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) as persistent complex bereavement disorder (PCBD), but its criteria remain debated. The condition has been studied using network analysis, showing potential for an improved understanding of PCBD. However, previous studies were limited to self-report and primarily originated from a single archival dataset. To overcome these limitations, we collected structured clinical interview data from a community sample of newly conjugally bereaved individuals (N = 305). Methods Gaussian graphical models (GGM) were estimated from PCBD symptoms diagnosed at 3, 14, and 25 months after the loss. A directed acyclic graph (DAG) was generated from initial PCBD symptoms, and comorbidity networks with DSM-5 symptoms of major depressive disorder (MDD) and post-traumatic stress disorder (PTSD) were analyzed 1 year post-loss. Results In the GGM, symptoms from the social/identity PCBD symptoms cluster (i.e. role confusion, meaninglessness, and loneliness) tended to be central in the network at all assessments. In the DAG, yearning activated a cascade of PCBD symptoms, suggesting how symptoms lead into psychopathological configurations. In the comorbidity networks, PCBD and depressive symptoms formed separate communities, while PTSD symptoms divided in heterogeneous clusters. Conclusions The network approach offered insights regarding the core symptoms of PCBD and the role of persistent yearnings. Findings are discussed regarding both clinical and theoretical implications that will serve as a step toward a more integrated understanding of PCBD.
Analytical Models of the Performance of C-V2X Mode 4 Vehicular Communications

The C-V2X or LTE-V standard has been designed to support vehicle to everything (V2X) communications. The standard is an evolution of LTE, and it has been published by the 3GPP in Release 14. This new standard introduces the C-V2X or LTE-V Mode 4 that is specifically designed for V2V communications using the PC5 sidelink interface without any cellular infrastructure support. In Mode 4, vehicles autonomously select and manage their radio resources. Mode 4 is highly relevant since V2V safety applications cannot depend on the availability of infrastructure-based cellular coverage. This paper presents the first analytical models of the communication performance of C-V2X or LTE-V Mode 4. In particular, the paper presents analytical models for the average packet delivery ratio (PDR) as a function of the distance between transmitter and receiver, and for the four different types of transmission errors that can be encountered in C-V2X Mode 4. The models are validated for a wide range of transmission parameters and traffic densities. To this aim, this study compares the results obtained with the analytical models to those obtained with a C-V2X Mode 4 simulator implemented over Veins.
Seroprevalence of Toxoplasma gondii in commensal rodents sampled across Senegal, West Africa

Risks related to Toxoplasma gondii infection in humans remain poorly known in Senegal. Although rodent surveys could help to assess the circulation of T. gondii, they have seldom been set up in sub-Saharan Africa. The aim of this study was to examine Toxoplasma seroprevalence in rodents from villages and towns across Senegal. Rodents were sampled in 40 localities using a standardised trapping protocol. Detection of T. gondii antibodies was performed on 1205 rodents, using a modified agglutination test (MAT) technique. Seroprevalence data were analysed depending on geography, the local rodent community, and individual characteristics of the rodent hosts. We found 44 seropositive rodents from four different species (Mastomys erythroleucus, Mastomys natalensis, Mus musculus domesticus, Rattus rattus). Toxoplasma seroprevalence was low, averaging 4% in the localities. Higher Toxoplasma seroprevalence (up to 24%) was found in northern Senegal, a region known to be the heart of pastoral herding in the country.
Molecular properties underlying regional vulnerability to Alzheimer’s disease pathology

See Lowe et al. (doi:10.1093/brain/awy226) for a scientific commentary on this article. Alzheimer’s disease targets discrete neural systems, but the mechanisms underlying this regionally selective vulnerability remain unknown. Grothe et al. report that Alzheimer’s disease pathology specifically affects brain regions with certain molecular properties, and that the biological pathways underlying this vulnerability differ for amyloid accumulation versus neurodegeneration.
CalR: A Web-based Analysis Tool for Indirect Calorimetry Experiments

We report a web-based tool for analysis of indirect calorimetry experiments which measure physiological energy balance. CalR easily imports raw data files, generates plots, and determines the most appropriate statistical tests for interpretation. Analysis with the general linear model (which includes ANOVA and ANCOVA) allows for flexibility to interpret experiments of obesity and thermogenesis. Users may also produce standardized output files of an experiment which can be shared and subsequently re-evaluated using CalR. This framework will provide the transparency necessary to enhance consistency and reproducibility in experiments of energy expenditure. CalR analysis software will greatly increase the speed and efficiency with which metabolic experiments can be organized, analyzed according to accepted norms, and reproduced—and will likely become a standard tool for the field. CalR is accessible at https://CalR.bwh. harvard.edu. Graphical Abstract
Platelet activation markers in children with congenital heart disease associated with pulmonary arterial hypertension

BACKGROUND Mean platelet volume (MPV), platecrit, and platelet distribution width (PDW) are markers of platelet activation. Previous studies have found that platelet activation occurs in patients with pulmonary arterial hypertension. Platelet indices including MPV, PDW, and platecrit have not been studied in children with congenital heart disease associated pulmonary arterial hypertension (APAH-CHD) who survived and those who died. OBJECTIVE The objective of this study to investigate the value of platelet indices with clinical and hemodynamic indicators predicting the disease severity and survival in children with APAH-CHD. METHODS This was a nested case-control study. MPV, platecrit, and PDW levels measured in 37 patients with APAH-CHD and 43 healthy subjects at the beginning of the study. Right heart catheterization was performed in all 37 patients. Clinical and hemodynamic data were collected. All patients were followed from the date of laboratory testing. The study was conducted between March 2012-July 2015. The comparison of clinical, hemodynamic data and platelet indices were made between patients with APAH-CHD who died than APAH-CHD patients who survived. RESULTS Of 37 patients, after a mean follow-up duration of 67.90 ± 47.90 months, 11 patients died. MPV (12.10 femoliter [fL; 8.20-12.50] vs 8.70 fL [6.40-9.70], P = .007), PDW (16.88 ± 1.09% vs 15.75 ± 1.58%, P = .04) and platecrit (0.28 ± 0.31 vs 0.22 ± 0.27, P = .01) were significantly higher in the patients with APAH-CHD who died than those who survived. Pearson's correlation analysis showed that MPV correlated with mean pulmonary artery pressure (r = 0.332, P = .04) and correlated negatively with six-minute walking distance (r = -0.600. P = .00). PDW and platecrit correlated positively with mean pulmonary artery pressure (r = 0.373, P = .02; r = 0.389, P = .01, respectively). CONCLUSION Our results showed that MPV, platecrit and PDW were increased in children with APAH-CHD. They might give clue about disease severity.
Mild hydrostatic pressure triggers oxidative responses in Escherichia coli

Hydrostatic pressure is an important physical stimulus which can cause various responses in bacterial cells. The survival and cellular processes of Escherichia coli under hydrostatic pressures between 10 MPa and 110 MPa have been studied. However, understanding bacterial responses to moderately elevated pressure of up to 10 MPa is useful for a range of different applications including for example in smart and responsive materials. In this study, the genetic responses of E. coli K-12 MG1655 to 1 MPa pressure was examined using transcriptomic analysis by RNA-Seq. The results show that 101 genes were differentially expressed under 1 MPa pressure in E. coli cells, with 85 of them up-regulated. The analysis suggested that some genes were over expressed to adapt the increase of oxygen levels in our system, and several functional categories are involved including oxidative stress responses, Fe-S cluster assembly and iron acquisition. Two differentially expressed genes azuC and entC were further investigated using RT-qPCR, and GFP reported strains of those two genes were created, AG1319 (PazuC azuC-msfgfp) and AG1321 (PentC entC-msfgfp). A linear response of azuC expression was observed between 0 MPa to 1 MPa by monitoring the fluorescence signal of strain AG1319 (PazuC azuC-msfgfp). This study is the first report to demonstrate the genetic response of bacterial cells under 1 MPa hydrostatic pressure, and provides preliminary data for creating pressure sensing bacterial strains for a wide range of applications.
The effect of intrapulmonary percussive ventilation in pediatric patients: A systematic review

Intrapulmonary percussive ventilation (IPV) is frequently used in clinical practice to enhance sputum evacuation and lung recruitment. However, the evidence in different respiratory pathologies, especially in children, is still lacking. This systematic review aims to enlist the effectiveness of IPV as an airway clearance technique in pediatric patients.
Video Versus Direct Laryngoscopy for Inpatient Emergency Intubation in Adults.

BACKGROUND Emergency intubation carries a higher risk of complications than elective airway management. Video laryngoscopy (VL) could potentially improve patient safety. The goal of this study was to determine whether VL is superior to direct laryngoscopy for the emergency intubation of adults in the inpatient setting. METHODS Pertinent studies were retrieved by a systematic literature search in the MEDLINE, Embase, and CENTRAL databases. The selection of studies, data extraction, and assessment of the potential for bias were carried out independently by two of the authors. Effect sizes were reported as odds ratios (OR) or mean differences (MD). The primary endpoint was successful intubation at the first attempt. Further variables were considered as secondary endpoints. RESULTS 1098 titles and abstracts were retrieved, and the full texts of 43 articles were examined. Eight randomized and controlled trials, with a total of 1796 patients, were analyzed. VL was not found to confer any statistically significant advantage with respect to successful intubation at the first attempt (OR 0.72, 95% confidence interval [0.47; 1.12]) or with respect to the time to successful intubation (MD -8.99 seconds [-24.00; 6.01]). On the other hand, the use of VL was significantly associated with a lower number of intubation attempts (MD -0.17 [-0.31; -0.03]) and with a lower frequency of esophageal intubation (OR 0.27 [0.10; 0.75]). CONCLUSION The routine use of VL for airway management in emergency medicine might improve patient safety, as VL is associated with a lower number of intubation attempts and with a lower frequency of esophageal intubation. Further randomized controlled trials are needed before any definitive conclusions can be drawn about the advantages of video laryngoscopy.
Generalized-ICP Aleksandr

In this paper we combine the Iterative Closest Point (’ICP’) and ‘point-to-plane ICP‘ algorithms into a single probabilistic framework. We then use this framework to model locally planar surface structure from both scans instead of just the ”model” scan as is typically done with the point-to-plane method. This can be thought of as ‘plane-to-plane’. The new approach is tested with both simulated and real-world data and is shown to outperform both standard ICP and point-to-plane. Furthermore, the new approach is shown to be more robust to incorrect correspondences, and thus makes it easier to tune the maximum match distance parameter present in most variants of ICP. In addition to the demonstrated performance improvement, the proposed model allows for more expressive probabilistic models to be incorporated into the ICP framework. While maintaining the speed and simplicity of ICP, the Generalized-ICP could also allow for the addition of outlier terms, measurement noise, and other probabilistic techniques to increase robustness.