Miracle-dz/UniFAR-FTUs huggingface dataset:
Water Flow and Heat Transport in Frozen Soil: Numerical Solution and Freeze–Thaw Applications

A new method is presented to account for phase changes in a fully implicit numerical model for coupled heat transport and variably saturated water flow involving conditions both above and below zero temperature. The method is based on a mixed formulation for both water flow and heat transport similar to the approach commonly used for the Richards equation. The approach enabled numerically stable, energy‐ and mass‐conservative solutions. The model was evaluated by comparing predictions with data from laboratory column freezing experiments. These experiments involved 20‐cm long soil columns with an internal diameter of 8 cm that were exposed at the top to a circulating fluid with a temperature of −6°C. Water and soil in the columns froze from the top down during the experiment, with the freezing process inducing significant water redistribution within the soil. A new function is proposed to better describe the dependency of the thermal conductivity on the ice and water contents of frozen soils. Predicted values of the total water content compared well with measured values. The model proved to be numerically stable also for a hypothetical road problem involving simultaneous heat transport and water flow. The problem was simulated using measured values of the surface temperature for the duration of almost 1 yr. Since the road was snow‐plowed during winter, surface temperatures varied more rapidly, and reached much lower values, than would have been the case under a natural snow cover. The numerical experiments demonstrate the ability of the code to cope with rapidly changing boundary conditions and very nonlinear water content and pressure head distributions in the soil profile.
2D Nanoclay for Biomedical Applications: Regenerative Medicine, Therapeutic Delivery, and Additive Manufacturing

Clay nanomaterials are an emerging class of 2D biomaterials of interest due to their atomically thin layered structure, charged characteristics, and well‐defined composition. Synthetic nanoclays are plate‐like polyions composed of simple or complex salts of silicic acids with a heterogeneous charge distribution and patchy interactions. Due to their biocompatible characteristics, unique shape, high surface‐to‐volume ratio, and charge, nanoclays are investigated for various biomedical applications. Here, a critical overview of the physical, chemical, and physiological interactions of nanoclay with biological moieties, including cells, proteins, and polymers, is provided. The state‐of‐the‐art biomedical applications of 2D nanoclay in regenerative medicine, therapeutic delivery, and additive manufacturing are reviewed. In addition, recent developments that are shaping this emerging field are discussed and promising new research directions for 2D nanoclay‐based biomaterials are identified.
A Systematic Review and Meta-analysis of the Diagnostic Accuracy of Nucleic Acid Amplification Tests for Tuberculous Meningitis

The diagnosis of tuberculous meningitis (TBM) is difficult and poses a significant challenge to physicians worldwide. Recently, nucleic acid amplification (NAA) tests have shown promise for the diagnosis of TBM, although their performance has been variable. ABSTRACT The diagnosis of tuberculous meningitis (TBM) is difficult and poses a significant challenge to physicians worldwide. Recently, nucleic acid amplification (NAA) tests have shown promise for the diagnosis of TBM, although their performance has been variable. We undertook a systematic review and meta-analysis to evaluate the diagnostic accuracy of NAA tests with cerebrospinal fluid (CSF) samples against that of culture as the reference standard or a combined reference standard (CRS) for TBM. We searched the Embase, PubMed, Web of Science, and Cochrane Library databases for the relevant records. The QUADAS-2 tool was used to assess the quality of the studies. Diagnostic accuracy measures (i.e., sensitivity and specificity) were pooled with a random-effects model. All statistical analyses were performed with STATA (version 14 IC; Stata Corporation, College Station, TX, USA), Meta-DiSc (version 1.4 for Windows; Cochrane Colloquium, Barcelona, Spain), and RevMan (version 5.3; The Nordic Cochrane Centre, the Cochrane Collaboration, Copenhagen, Denmark) software. Sixty-three studies comprising 1,381 cases of confirmed TBM and 5,712 non-TBM controls were included in the final analysis. These 63 studies were divided into two groups comprising 71 data sets (43 in-house tests and 28 commercial tests) that used culture as the reference standard and 24 data sets (21 in-house tests and 3 commercial tests) that used a CRS. Studies which used a culture reference standard had better pooled summary estimates than studies which used CRS. The overall pooled estimates of sensitivity, specificity, positive likelihood ratio (PLR), and negative likelihood ratio (NLR) of the NAA tests against culture were 82% (95% confidence interval [CI], 75 to 87%), 99% (95% CI, 98 to 99%), 58.6 (95% CI, 35.3 to 97.3), and 0.19 (95% CI, 0.14 to 0.25), respectively. The pooled sensitivity, specificity, PLR, and NLR of NAA tests against CRS were 68% (95% CI, 41 to 87%), 98% (95% CI, 95 to 99%), 36.5 (95% CI, 15.6 to 85.3), and 0.32 (95% CI, 0.15 to 0.70), respectively. The analysis has demonstrated that the diagnostic accuracy of NAA tests is currently insufficient for them to replace culture as a lone diagnostic test. NAA tests may be used in combination with culture due to the advantage of time to result and in scenarios where culture tests are not feasible. Further work to improve NAA tests would benefit from the availability of standardized reference standards and improvements to the methodology.
Percutaneous Endoscopic Decompression in Lumbar Canal and Lateral Recess Stenosis – The Surgical Learning Curve

Objective The purpose of this study is to characterize the learning curve of endoscopic lumbar decompression based on peri- and postoperative parameters and to suggest the potential of full endoscopic decompression as a primary treatment option for lumbar canal and lateral recess stenosis. Methods The records of 223 consecutive patients who underwent percutaneous endoscopic decompression by a single surgeon for their lumbar canal and lateral recess stenosis were reviewed. Patients were stratified into group 1 (n=100) and group 2 (n=123), depending on their case number. After the 100th case, the procedural time reached a plateau and subsequent patients were assigned to the second group. Demographics and surgical outcomes, including operative times, change in dural sac dimensions, length of hospital stay, and intraoperative complication rates were compared between the 2 groups. Postoperative clinical outcomes, including the visual analogue scale (VAS), the Oswestry Disability Index (ODI) and reoperation rates were compared between the 2 groups (group 1, n=90; group 2, n=110) by follow-up evaluation. Results Procedural times were greater in group 1 than group 2 (group 1, 105.26 minutes; group 2, 67.65 minutes; p<0.05) and they had higher complication rates (group 1, 16% [16 of 100]; group 2, 8.3% [8 of 123]; p<0.05). The length of hospitalization, postoperative improvement in VAS and ODI, and reoperation rates were not different between the groups. In both groups, stenotic spinal canals were effectively decompressed. Conclusion Continued surgical experience was associated with a reduction in operative times and less intraoperative complications. Although the learning curve was steep and additional surgical experience may be needed to overcome the learning curve, percutaneous full endoscopic lumbar decompression is a safe, clinically-feasible, and effective surgical technique and can be adopted as the primary treatment for lumbar canal and lateral recess stenosis.
A Self-Reliant Umbrella: Defining Successful Aging Among the Old-Old (80+) in Shanghai

The Chinese old-old (80+) population has steadily increased in recent years; however, limited studies have examined how this group ages. The purpose of this study is to explore how the old-old in urban China define successful aging. Guided by grounded theory, we conducted semi-structured, in-depth interviews with community-dwelling old-old participants (N = 97). Participants identified self-reliance as the goal of successful aging, which was supported by four proactive behaviors: physical activity, financial security, community connectedness, and willing acceptance of reality. In our model, we conceptualized these four proactive behaviors to constitute the ribs of an umbrella, supporting a canopy to protect the pole of self-reliant successful aging. This study offers new understanding of the dynamic and nuanced ways that the old-old in urban China age successfully and of their valiant efforts to maintain self-reliance.
The VIRMOS deep imaging survey - I. Overview, survey strategy, and CFH12K observations

This paper presents the CFH12K-VIRMOS survey: a deep B, V, R and I imaging survey in four fields totalling more than 17 deg^2, conducted with the 30x40 arcmin^2 field CFH-12K camera. The survey is intended to be a multi-purpose survey used for a variety of science goals, including surveys of very high redshift galaxies and weak lensing studies. Four high galactic latitude fields, each 2x2 deg^2, have been selected along the celestial equator: 0226-04, 1003+01, 1400+05, and 2217+00. The 16 deg^2 of the "wide" survey are covered with exposure times of 2h, 1.5h, 1h, 1h, while the 1.3x1 deg^2 area of the "deep" survey at the center of the 0226-04 field is covered with exposure times of 7h, 4.5h, 3h, 3h, in B,V,R and I respectively. The data is pipeline processed at the Terapix facility at the Institut d'Astrophysique de Paris to produce large mosaic images. The catalogs produced contain the positions, shape, total and aperture magnitudes for the 2.175 million objects. The depth measured (3sigma in a 3 arc-second aperture) is I_{AB}=24.8 in the ``Wide'' areas, and I_{AB}=25.3 in the deep area. Careful quality control has been applied on the data as described in joint papers. These catalogs are used to select targets for the VIRMOS-VLT Deep Survey, a large spectroscopic survey of the distant universe (Le Fevre et al., 2003). First results from the CFH12K-VIRMOS survey have been published on weak lensing (e.g. van Waerbeke & Mellier 2003). Catalogs and images are available through the VIRMOS database environment under Oracle ({\tt http://www.oamp.fr/virmos}). They will be open for general use on July 1st, 2003.
Evolutionary relationship analysis of Middle East respiratory syndrome coronavirus 4a and 4b protein coding sequences

The 4a and 4b proteins of the Middle East respiratory syndrome coronavirus (MERS-CoV) have been described for their antagonism on host innate immunity. However, unlike clustering patterns of the complete gene sequences of human and camel MERS-CoVs, the 4a and 4b protein coding regions did not constitute species-specific phylogenetic groups. Moreover, given the estimated evolutionary rates of the complete, 4a, and 4b gene sequences, the 4a and 4b proteins might be less affected by species-specific innate immune pressures. These results suggest that the 4a and 4b proteins of MERS-CoV may function against host innate immunity in a manner independent of host species and/or evolutionary clustering patterns.
Abdominal aortic calcification, bone mineral density and fractures: a systematic review and meta-analysis protocol

Introduction Abdominal aortic calcification (AAC) is associated with low bone mass and increased fracture risk. Two previous meta-analyses have investigated the association between AAC and fracture. However, these meta-analyses only identified articles until December 2016, undertook limited searches and did not explore potential sources of between-study heterogeneity. We aim to undertake a sensitive and comprehensive assessment of the relationship between AAC, bone mineral density (BMD) as well as prevalent and incident fractures. Methods We will search MEDLINE, EMBASE, Web of Science core collection and Google Scholar (top 200 articles sorted by relevance) from their inception to 1 June 2018. Reference lists of included studies and previous systematic reviews will be hand searched for additional eligible studies. Retrospective and prospective cohort studies (cross-sectional, case–control and longitudinal) reporting the association between AAC, BMD and fracture at any site will be included. At least two investigators will independently: (A) evaluate study eligibility and extract data, with a third investigator to adjudicate when discrepancies occur, (B) assess study quality by the Newcastle-Ottawa Scale for each cohort/study. The meta-analysis will be reported in adherence to the Meta-analysis of Observational Studies in Epidemiology criteria. AAC will be grouped as either: (1) AAC present or absent, (2) AAC categorised as ‘low’ (referent—lowest reported group) versus ‘high’ (all other groups) or (3) dose–response when AAC was assessed in ≥3 groups. Where primary event data were reported in individual studies, pooled risk differences and risk ratios with 95% CI will be calculated, from which, a summary estimate will be determined using DerSimonian-Laird random effects models. For the AAC and BMD pooled analyses, estimates will be expressed as standardised mean difference with 95% CI. We will examine the likelihood of publication bias and where possible, investigate potential reasons for between-study heterogeneity using subgroup analyses and meta-regression. Ethics and dissemination The study will be submitted to a peer- reviewed journal and disseminated via research presentations. PROSPERO registration number CRD42018088019.
The Superficial Face Dissection as an Example for Integrating Clinical Approaches, Authentic Learning, and Changing Perspectives in Anatomy Dissection

Hands‐on dissection‐based learning of anatomy offers an unique and valued experience for medical students. Too often however, the inexperienced student's focus is to avoid damage to unfamiliar structures instead of understanding spatial relationships between structures. This results in unfortunate surrender of a critical learning experience. Additionally, approaches to dissection and anatomic exposure share little alignment to clinical approaches, making it less powerful in clinical applicability. The goal of this viewpoint commentary is based on the experience of the two authors and aims to demonstrate opportunity to introduce clinical approaches for dissection while incorporating relevant anatomical concepts in medical school curriculum that aligns with authentic healthcare practice. Using the dissections of the superficial face as a relevant and current topic of clinical interest, we point out that applying the currently performed dissection approach (medial‐to‐lateral) falls short of providing sufficient knowledge and understanding of the layered arrangement of facial structures. The lateral‐to‐medial approach, as performed in surgical face lifting procedures would offer a better understanding of the layers of the face and especially the superficial musculoaponeurotic system (SMAS) accounting for the difficulties of facial dissections on embalmed cadavers. This commentary could offer a potential change in paradigm for students and course facilitators for how to maximize the knowledge transfer during facial dissections. It potentially opens a door to rethink dissection‐based learning of anatomy toward techniques and approaches that are aligned to surgical access pathways and thus considered more clinically relevant.
Rates of and Factors Associated With Patient-reported Illicit Drug Use Screening by Health Care Professionals in the United States From 2013 to 2015.

OBJECTIVES To examine rates of and factors associated with patient-reported illicit drug use screening by health care professionals. METHODS The National Survey on Drug Use and Health (NSDUH), limited to individuals who reported prior year healthcare service utilization, was used to capture the odds of patient-reported illicit drug use screening for survey years 2013 to 2015. Screened patients were contrasted with those not screened by demographic and behavioral characteristics. Adjusted models were produced by year and adjusted odds ratios were compared for changes across years. A separate adjusted model including year as a fixed effect was produced to estimate changes in overall adjusted screening odds. RESULTS The percentage of individuals reporting screening by a health care provider increased from 48.5% in 2013 to 50.9% (2014), and 54.3% (2015) (P < 0.0001). The adjusted model, including year as a fixed effect, indicated that the odds of screening significantly increased from 2013 to 2015. In multivariable regression, individuals reporting screening were more likely to be female, of higher income and educational strata, and received drug or alcohol treatment in the past year and were less likely to be non-Hispanic Asian. CONCLUSIONS Only roughly half of individuals seen by a healthcare provider report illicit drug use screening. Racial disparities in screening persist although they are overall decreasing. Coupling screening with treatment initiation, rather than brief intervention, may increase screening rates.
The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy

The major coat proteins of dsDNA tailed phages (order Caudovirales) and herpesviruses form capsids by a mechanism that includes active packaging of the dsDNA genome into a precursor procapsid, followed by expansion and stabilization of the capsid. These viruses have evolved diverse strategies to fortify their capsids, such as non-covalent binding of auxiliary ‘decoration’ (Dec) proteins. The Dec protein from the P22-like phage L has a highly unusual binding strategy that distinguishes between nearly identical three-fold and quasi-three-fold sites of the icosahedral capsid. Cryo-electron microscopy and three-dimensional image reconstruction were employed to determine the structure of native phage L particles. NMR was used to determine the structure/dynamics of Dec in solution. The NMR structure and the cryo-EM density envelope were combined to build a model of the capsid-bound Dec trimer. Key regions that modulate the binding interface were verified by site-directed mutagenesis.
Co-culture of osteochondral explants and synovial membrane as in vitro model for osteoarthritis

The purpose of the current study was to establish an in vitro model for osteoarthritis (OA) by co-culture of osteochondral and synovial membrane explants. Osteochondral explants were cultured alone (control-1) or in co-culture with synovial membrane explants (control-2) in standard culture medium or with interleukin-1β (IL1β) and tumor necrosis factor (TNFα) added to the culture medium (OA-model-1 = osteochondral explant; OA-model-2 = osteochondroal-synovial explant). In addition, in OA-model groups a 2-mm partial-thickness defect was created in the centre of the cartilage explant. Changes in the expression of extracellular matrix (ECM) genes (collagen type-1 (Col1), Col2, Col10 and aggrecan) as well as presence and quantity of inflammatory marker genes (IL6, matrix metalloproteinase-1 (MMP1), MMP3, MMP13, a disintegrin and metalloproteinase with-thrombospondin-motif-5 (ADAMTS5) were analysed by immunohistochemistry, qPCR and ELISA. To monitor the activity of classically-activated pro-inflammatory (M1) versus alternatively-activated anti-inflammatory/repair (M2) synovial macrophages, the nitric oxide/urea ratio in the supernatant of osteochondral-synovial explant co-cultures was determined. In both OA-model groups immunohistochemistry and qPCR showed a significantly increased expression of MMPs and IL6 compared to their respective control group. ELISA results confirmed a statistically significant increase in MMP1and MMP3 production over the culturing period. In the osteochondral-synovial explant co-culture OA-model the nitric oxide/urea ratio was increased compared to the control group, indicating a shift toward M1 synovial macrophages. In summary, chemical damage (TNFα, IL1β) in combination with a partial-thickness cartilage defect elicits an inflammatory response similar to naturally occurring OA in osteochondral explants with and without osteochondral-synovial explant co-cultures and OA-model-2 showing a closer approximation of OA due to the additional shift of synovial macrophages toward the pro-inflammatory M1 phenotype.
Proposal of a Machine Learning Approach to Differentiate Mild and Alzheimer's Condition in MR Images Using Shape Changes in Corpus Callosum

The brain ventricles are surrounded by periventricular structures that are affected by dementia which results in neurodegenerative disorder such as Alzheimer's Disease (AD). The change in morphology of these structures must effect the shape and volume of Corpus Callosum (CC). These alterations in morphology of CC are considered to be a significant image biomarker for the early diagnosis of Mild Cognitive Impairment (MCI) and Alzheimer's disease (AD) subjects. Shape descriptors provide useful information about change in morphology of various brain structures during disease progression. In this work, Lattice Boltzmann criterion based hybrid level set method (LSM) is used to segment CC. Geometric and pseudo-Zernike moment measures are extracted from the segmented area of CC and are statistically analyzed using Statistical Package for Social Science (SPSS). The performance metric of significant moments is validated using machine learning algorithms. Results demonstrate that, hybrid level set is able to delineate CC and the segmented images are in high correlation with ground truth images. High accuracy value of 85.0% has been achieved using Multilayer Perceptron (MLP) classifier for Healthy Control (HC) versus AD subjects. Thus, moments are able to classify MCI from HC and AD subjects with high accuracy and hence the results are found to be clinically significant.
Micronutrient powder supplements combined with nutrition education marginally improve growth amongst children aged 6-23 months in rural Burkina Faso: A cluster randomized controlled trial.

Micronutrients powder (MNP) can prevent anaemia amongst children 6-23 months old. However, evidence of an effect on growth is limited and concerns about the safety of iron-containing MNP interventions limits their applicability. In a cluster randomized controlled intervention, we evaluated the effectiveness of a nutritional package including counselling and provision of MNP to improve the nutritional status of children aged 6-23 months and the effect of sustained use of MNP on morbidity in a malaria-endemic area. Child feeding practises and nutritional status were assessed through cross-sectional surveys. Biweekly morbidity surveillance and anthropometry measurements were carried out in a nested cohort study. No significant differences in the prevalence of wasting (-0.7% [-6.8, 5.3] points; p = .805), stunting (+4.6% [-2.9, 12.0] points; p = .201), or mean length-for-age z-score and weight-for-length z-score scores were found between study groups. The proportion of children with a minimum dietary diversity score and those with a minimum acceptable diet significantly increased in the intervention group compared with the control by 6.5% points (p = .043) and 5.8% points (p = .037), respectively. There were no significant differences in the risk of diarrhoea (RR: 1.68, 95% CI [0.94, 3.08]), fever (RR: 1.20 [0.82, 1.77]), and malaria (RR: 0.68 [0.37, 1.26]) between study groups. In the nested study, the rate of linear growth was higher in the intervention than in the control group by 0.013 SD/month (p = .027). In a programmatic intervention, MNP and nutrition education marginally improved child feeding practises and growth, without increasing morbidity from malaria or fever.