Miracle-dz/UniFAR-FTUs huggingface dataset:
Longitudinal profiling of the lung microbiome in the AERIS study demonstrates repeatability of bacterial and eosinophilic COPD exacerbations

Background Alterations in the composition of the lung microbiome associated with adverse clinical outcomes, known as dysbiosis, have been implicated with disease severity and exacerbations in COPD. Objective To characterise longitudinal changes in the lung microbiome in the AERIS study (Acute Exacerbation and Respiratory InfectionS in COPD) and their relationship with associated COPD outcomes. Methods We surveyed 584 sputum samples from 101 patients with COPD to analyse the lung microbiome at both stable and exacerbation time points over 1 year using high-throughput sequencing of the 16S ribosomal RNA gene. We incorporated additional lung microbiology, blood markers and in-depth clinical assessments to classify COPD phenotypes. Results The stability of the lung microbiome over time was more likely to be decreased in exacerbations and within individuals with higher exacerbation frequencies. Analysis of exacerbation phenotypes using a Markov chain model revealed that bacterial and eosinophilic exacerbations were more likely to be repeated in subsequent exacerbations within a subject, whereas viral exacerbations were not more likely to be repeated. We also confirmed the association of bacterial genera, including Haemophilus and Moraxella, with disease severity, exacerbation events and bronchiectasis. Conclusions Subtypes of COPD have distinct bacterial compositions and stabilities over time. Some exacerbation subtypes have non-random probabilities of repeating those subtypes in the future. This study provides insights pertaining to the identification of bacterial targets in the lung and biomarkers to classify COPD subtypes and to determine appropriate treatments for the patient. Trial registration number Results, NCT01360398.
Acute Compartment Syndrome: An Expert Survey of Orthopaedic Trauma Association Members

Objectives: The goal of this study was to describe current opinions of orthopaedic trauma experts regarding acute compartment syndrome (ACS). Design: Web-based survey. Participants: Active Orthopaedic Trauma Association (OTA) members. Methods: A 25-item web-based questionnaire was advertised to active members of the OTA. Using a cross-sectional survey study design, we evaluated the perceived importance of ACS, as well as preferences in diagnosis and treatment. Results: One hundred thirty-nine of 596 active OTA members (23%) completed the survey. ACS was believed to be clinically important and with severe sequelae, if missed. Responses indicated that diagnosis should be based on physical examination in an awake patient, and that intracompartmental pressure testing was valuable in the obtunded or unconscious patient. The diagnosis of ACS with monitoring should be made using the difference between diastolic blood pressure and intracompartmental pressure (&Dgr;P) of ⩽30 mm Hg. Once ACS is diagnosed, respondents indicated that fasciotomies should be performed as quickly as is reasonable (within 2 hours). The consensus for wound management was closure or skin grafting within 1–5 days later, and skin grafting was universally recommended if closure was delayed to >7 days. Conclusions: ACS is a challenging problem with poor outcomes if missed or inadequately treated. OTA members demonstrated agreement to many diagnostic and treatment choices for ACS. Level of Evidence: Therapeutic Level V. See Instructions for Authors for a complete description of the levels of evidence.
Zika Virus Shedding in Semen of Symptomatic Infected Men

Background Zika virus (ZIKV) is an emerging mosquito‐borne flavivirus that has been linked to adverse birth outcomes. Previous reports have shown that person‐to‐person transmission can occur by means of sexual contact. Methods We conducted a prospective study involving men with symptomatic ZIKV infection to determine the frequency and duration of ZIKV shedding in semen and urine and to identify risk factors for prolonged shedding in these fluids. Specimens were obtained twice per month for 6 months after illness onset and were tested by real‐time reverse‐transcriptase–polymerase‐chain‐reaction (RT‐PCR) assay for ZIKV RNA and by Vero cell culture and plaque assay for infectious ZIKV. Results A total of 1327 semen samples from 184 men and 1038 urine samples from 183 men were obtained 14 to 304 days after illness onset. ZIKV RNA was detected in the urine of 7 men (4%) and in the semen of 60 (33%), including in semen samples from 22 of 36 men (61%) who were tested within 30 days after illness onset. ZIKV RNA shedding in semen decreased substantially during the 3 months after illness onset but continued for 281 days in 1 man (1%). Factors that were independently associated with prolonged RNA shedding included older age, less frequent ejaculation, and the presence of certain symptoms at the time of initial illness. Infectious ZIKV was isolated from 3 of 78 semen samples with detectable ZIKV RNA, all obtained within 30 days after illness onset and all with at least 7.0 log10 ZIKV RNA copies per milliliter of semen. Conclusions ZIKV RNA was commonly present in the semen of men with symptomatic ZIKV infection and persisted in some men for more than 6 months. In contrast, shedding of infectious ZIKV appeared to be much less common and was limited to the first few weeks after illness onset. (Funded by the Centers for Disease Control and Prevention.)
3D-MAPS: 3D Massively parallel processor with stacked memory

Several recent works have demonstrated the benefits of through-silicon-via (TSV) based 3D integration, but none of them involves a fully functioning multicore processor and memory stacking. 3D-MAPS (3D Massively Parallel Processor with Stacked Memory) is a two-tier 3D IC, where the logic die consists of 64 general-purpose processor cores running at 277MHz, and the memory die contains 256KB SRAM. Fabrication is done using 130nm GlobalFoundries device technology and Tezzaron TSV and bonding technology. Packaging is done by Amkor. This processor contains 33M transistors, 50K TSVs, and 50K face-to-face connections in 5x5mm2 footprint. The chip runs at 1.5V and consumes up to 4W, resulting in 16W/cm2 power density. The core architecture is developed from scratch to benefit from single-cycle access to SRAM.
Enrofloxacin and Macrolides Alone or in Combination with Rifampicin as Antimicrobial Treatment in a Bovine Model of Acute Chlamydia psittaci Infection

Chlamydia psittaci is a zoonotic bacterium with a wide host range that can cause respiratory disease in humans and cattle. In the present study, effects of treatment with macrolides and quinolones applied alone or in combination with rifampicin were tested in a previously established bovine model of respiratory C. psittaci infection. Fifty animals were inoculated intrabronchially at the age of 6–8 weeks. Seven served as untreated controls, the others were assigned to seven treatment groups: (i) rifampicin, (ii) enrofloxacin, (iii) enrofloxacin + rifampicin, (iv) azithromycin, (v) azithromycin + rifampicin, (vi) erythromycin, and (vii) erythromycin + rifampicin. Treatment started 30 hours after inoculation and continued until 14 days after inoculation (dpi), when all animals were necropsied. The infection was successful in all animals and sufficient antibiotic levels were detected in blood plasma and tissue of the treated animals. Reisolation of the pathogen was achieved more often from untreated animals than from other groups. Nevertheless, pathogen detection by PCR was possible to the same extent in all animals and there were no significant differences between treated and untreated animals in terms of local (i.e. cell count and differentiation of BALF-cells) and systemic inflammation (i.e. white blood cells and concentration of acute phase protein LBP), clinical signs, and pathological findings at necropsy. Regardless of the reduced reisolation rate in treated animals, the treatment of experimentally induced respiratory C. psittaci infection with enrofloxacin, azithromycin or erythromycin alone or in combination with rifampicin was without obvious benefit for the host, since no significant differences in clinical and pathological findings or inflammatory parameters were detected and all animals recovered clinically within two weeks.
Fully Automatic Segmentation of Sphenoid Sinus in CT Images with 3D Convolutional Neural Networks

Today, Deep learning algorithms have quickly become essential in the field of medical image analysis. Compared to the traditional methods, these Deep learning techniques are more efficient in extracting compact information leading towards significant improvement performance of medical image analysis system. We present in this paper a new technique for sphenoid sinus automatic segmentation using a 3D Convolutional Neural Networks (CNN). Due to the scarcity of medical data, we chose to used a 3D CNN model learned on a small training set. Mathematical morphology operations are then used to automatically detect and segment the region of interest. Our proposed method is tested and compared with a semi-automatic method and manual delineations made by a specialist. The preliminary results from the Computed Tomography (CT) volumes seem to be very promising.
Wnt/ß-catenin/Lef-1 signaling in the uterus and its implications in uterine gland formation and cancer development

Wnt/b-catenin signaling appears to be important in a multitude of cancers. This review article details current knowledge of the Wnt/b-catenin/Lef1 pathway in generalized gland regulation and formation in addition to endometrial cancer. Wnt signaling is critical for the development of the female urogenital system, in particular mullerian duct formation. Dysregulation of this signaling pathway at multiple nodes has been observed in numerous tumor types, including endometrial cancer. In particular, nuclear accumulation of b-catenin correlates with tumor severity. As such, therapeutic modulation of Wnt signaling represents an emerging avenue for the treatment of cancers that rely on this pathway. The Department of Obstetrics and Gynecology, The Carver College of Medicine, The University of Iowa, Iowa City,
Operational High Resolution Land Cover Map Production at the Country Scale Using Satellite Image Time Series

A detailed and accurate knowledge of land cover is crucial for many scientific and operational applications, and as such, it has been identified as an Essential Climate Variable. This accurate knowledge needs frequent updates. This paper presents a methodology for the fully automatic production of land cover maps at country scale using high resolution optical image time series which is based on supervised classification and uses existing databases as reference data for training and validation. The originality of the approach resides in the use of all available image data, a simple pre-processing step leading to a homogeneous set of acquisition dates over the whole area and the use of a supervised classifier which is robust to errors in the reference data. The produced maps have a kappa coefficient of 0.86 with 17 land cover classes. The processing is efficient, allowing a fast delivery of the maps after the acquisition of the image data, does not need expensive field surveys for model calibration and validation, nor human operators for decision making, and uses open and freely available imagery. The land cover maps are provided with a confidence map which gives information at the pixel level about the expected quality of the result.
MoS2-based nanocomposites for surface enhanced Raman scattering

Molybdenum disulfide (MoS2) monolayer, a two dimensional (2D) layered transition metal dichalcogenides with its novel nanoelectronic and optoelectronic properties has been investigated and applied widely. MoS2-based hybrid composites have shown great potential in chemical and biological fields by combining the advantages of several structures. In our work, a SERS-active substrate was fabricated by combining the MoS2 monolayer with Ag Nanowire (NW)−Nanoparticle (NP) structures using a spin-coated method. This AgNW−AgNP−MoS2 hybrid structure was characterized by SEM, UV-Vis and Raman spectroscopy. Experimental results indicate that strong SERS signals of rhodamine 6G (R6G) molecules is able to be achieved at the “hotspot” formed in this hybrid structure. The enhancement factor is high up to 106 as the incident laser is polarized perpendicular to the NW and the limit of detection is found to be as low as 10-11 M. Besides, the fabricated SERS substrate was reliable and reproducible, which showed great potential to be an excellent SERS substrate for chemical and biological detection.
Laboratory and Field Evaluation of the Partec CyFlow MiniPOC for Absolute and Relative CD4 T-Cell Enumeration

Background A new CD4 point-of-care instrument, the CyFlow miniPOC, which provides absolute and percentage CD4 T-cells, used for screening and monitoring of HIV-infected patients in resource-limited settings, was introduced recently. We assessed the performance of this novel instrument in a reference laboratory and in a field setting in Senegal. Methodology A total of 321 blood samples were obtained from 297 adults and 24 children, all HIV-patients attending university hospitals in Dakar, or health centers in Ziguinchor. Samples were analyzed in parallel on CyFlow miniPOC, FACSCount CD4 and FACSCalibur to assess CyFlow miniPOC precision and accuracy. Results At the reference lab, CyFlow miniPOC, compared to FACSCalibur, showed an absolute mean bias of -12.6 cells/mm3 and a corresponding relative mean bias of -2.3% for absolute CD4 counts. For CD4 percentages, the absolute mean bias was -0.1%. Compared to FACSCount CD4, the absolute and relative mean biases were -31.2 cells/mm3 and -4.7%, respectively, for CD4 counts, whereas the absolute mean bias for CD4 percentages was 1.3%. The CyFlow miniPOC was able to classify HIV-patients eligible for ART with a sensitivity of ≥ 95% at the different ART-initiation thresholds (200, 350 and 500 CD4 cells/mm3). In the field lab, the room temperature ranged from 30 to 35°C during the working hours. At those temperatures, the CyFlow miniPOC, compared to FACSCount CD4, had an absolute and relative mean bias of 7.6 cells/mm3 and 2.8%, respectively, for absolute CD4 counts, and an absolute mean bias of 0.4% for CD4 percentages. The CyFlow miniPOC showed sensitivity equal or greater than 94%. Conclusion The CyFlow miniPOC showed high agreement with FACSCalibur and FACSCount CD4. The CyFlow miniPOC provides both reliable absolute CD4 counts and CD4 percentages even under the field conditions, and is suitable for monitoring HIV-infected patients in resource-limited settings.
The Semi-Virtual Violin – A Perception Tool

In this paper, a semi-virtual violin is presented which has been developed in the context of a research project on desirable violin sound properties. The method used here focuses on musicians’ perception of spectral components rather than on physical modeling properties. A silent violin which has been designed with particular emphasis on authentic haptic and visual properties is used as interface between musician and virtual body. Binaural transfer functions of real violins measured at the violinist’s hearing position serve as initial sound references for further spectral modifications. A filtering software enables highly-detailed modifications in the frequency domain, changing individual resonances or resonance areas while leaving other resonances unaffected. Implementation on an external signal processor provides for real-time sound processing. An application example demonstrates the tools capability: The presented tool can be used, inter alia, to manipulate the vowel quality in violin tones by modifying specific formant properties.
Advantages and limitations of the protein digestibility-corrected amino acid score (PDCAAS) as a method for evaluating protein quality in human diets

PDCAAS is a widely used assay for evaluating protein quality. It is a chemical score, which is derived from the ratio between the first limiting amino acid in a test protein and the corresponding amino acid in a reference amino acid pattern and corrected for true faecal N digestibility. Chemical scores exceeding 100 % are truncated to 100 %. The advantages of the PDCAAS are its simplicity and direct relationship to human protein requirements. The limitations are as follows: the reference pattern is based on the minimum amino acid requirements for tissue growth and maintenance and does not necessarily reflect the optimum intake. Truncated PDCAAS of high-quality proteins do not give any information about the power of these proteins to compensate, as a supplement, for low levels of dietary essential amino acids in low-quality proteins. It is likely that faecal N digestibility does not take into account the loss from the colon of indispensable amino acids that were not absorbed in the ileum. Anti-nutritional factors, such as lectins and trypsin inhibitors, in several plant protein sources can cause heightened endogenous losses of amino acids, an issue which is particularly relevant in animal feedstuffs. The assumption that amino acid supplementation can completely restore biological efficiency of the protein source is incorrect since the kinetics of digestion and absorption between supplemented free amino acids and amino acids present in dietary proteins, are different.
Genomic DNA Methylation-Derived Algorithm Enables Accurate Detection of Malignant Prostate Tissues

Introduction The current methodology involving diagnosis of prostate cancer (PCa) relies on the pathology examination of prostate needle biopsies, a method with high false negative rates partly due to temporospatial, molecular, and morphological heterogeneity of prostate adenocarcinoma. It is postulated that molecular markers have a potential to assign diagnosis to a considerable portion of undetected prostate tumors. This study examines the genome-wide DNA methylation changes in PCa in search of genomic markers for the development of a diagnostic algorithm for PCa screening. Methods Archival PCa and normal tissues were assessed using genomic DNA methylation arrays. Differentially methylated sites and regions (DMRs) were used for functional assessment, gene-set enrichment and protein interaction analyses, and examination of transcription factor-binding patterns. Raw signal intensity data were used for identification of recurrent copy number variations (CNVs). Non-redundant fully differentiating cytosine-phosphate-guanine sites (CpGs), which did not overlap CNV segments, were used in an L1 regularized logistic regression model (LASSO) to train a classification algorithm. Validation of this algorithm was performed using a large external cohort of benign and tumor prostate arrays. Results Approximately 6,000 probes and 600 genomic regions showed significant DNA methylation changes, primarily involving hypermethylation. Gene-set enrichment and protein interaction analyses found an overrepresentation of genes related to cell communications, neurogenesis, and proliferation. Motif enrichment analysis demonstrated enrichment of tumor suppressor-binding sites nearby DMRs. Several of these regions were also found to contain copy number amplifications. Using four non-redundant fully differentiating CpGs, we trained a classification model with 100% accuracy in discriminating tumors from benign samples. Validation of this algorithm using an external cohort of 234 tumors and 92 benign samples yielded 96% sensitivity and 98% specificity. The model was found to be highly sensitive to detect metastatic lesions in bone, lymph node, and soft tissue, while being specific enough to differentiate the benign hyperplasia of prostate from tumor. Conclusion A considerable component of PCa DNA methylation profile represent driver events potentially established/maintained by disruption of tumor suppressor activity. As few as four CpGs from this profile can be used for screening of PCa.
Ranolazine: A true pluripotent cardiovascular drug or jack of all trades, master of none?

Cardiovascular disease (CVD) is a leading cause of morbidity and mortality worldwide. Although the majority of patients with CVD are treated with interventional procedures, a substantial number require medical therapy in terms of both prognosis and symptomatic relief. However, commonly used agents such as β-blockers and calcium channel blockers reduce blood pressure in patients whose resting pressures are often already low. Ranolazine is a promising agent that does not have significant effects on blood pressure or heart rate. Use of this drug has been documented in various cardiovascular conditions, including ischaemic heart disease, heart failure and arrhythmias. This review article aimed to examine current evidence on the use of ranolazine in various cardiovascular conditions in order to determine whether it is a true pluripotent cardiovascular agent or, on the other hand, a "jack of all trades, master of none. "
The Comorbidity Between Internet Gaming Disorder and Depression: Interrelationship and Neural Mechanisms

Internet gaming disorder (IGD) is characterized by cognitive and emotional deficits. Previous studies have reported the co-occurrence of IGD and depression. However, extant brain imaging research has largely focused on cognitive deficits in IGD. Few studies have addressed the comorbidity between IGD and depression symptoms and underlying neural mechanisms. Here, we systematically investigated this issue by combining a longitudinal survey study, a cross-sectional resting-state functional connectivity (rsFC) study and an intervention study. Autoregressive cross-lagged modeling on a longitudinal dataset of college students showed that IGD severity and depression are reciprocally predictive. At the neural level, individuals with IGD exhibited enhanced rsFC between the left amygdala and right dorsolateral prefrontal cortex (DLPFC), inferior frontal and precentral gyrus, compared with control participants, and the amygdala-frontoparietal connectivity at the baseline negatively predicted reduction in depression symptoms following a psychotherapy intervention. Further, following the intervention, individuals with IGD showed decreased connectivity between the left amygdala and left middle frontal and precentral gyrus, as compared with the non-intervention group. These findings together suggest that IGD may be closely associated with depression; aberrant rsFC between emotion and executive control networks may underlie depression and represent a therapeutic target in individuals with IGD. Registry name: The behavioral and brain mechanism of IGD; URL: https://www.clinicaltrials. gov/ct2/show/NCT02550405; Registration number: NCT02550405.
Revision surgery after rod breakage in a patient with occipitocervical fusion

Rationale: Rod breakage after occipitocervical fusion (OCF) has never been described in a patient who has undergone surgery for basilar invagination (BI) and atlantoaxial dislocation (AAD). Here, we present an unusual but significant case of revision surgery to correct this complication. Patient concerns: A 32-year-old female presented with neck pain, unstable leg motion in walking, and also BI with AAD. Her first surgery was planned to correct these conditions and for fusion at the occipital junction (C3-4) using a screw-rod system. At the 31-month follow-up after her first operation, the patient complained of severe neck pain and limitation of motion, suggesting rod breakage. Diagnoses: Rod breakage after occipitocervical fusion for BI and AAD. Interventions: The patient underwent reoperation for replacement of the broken rods, adjustment of the occipitocervical angle, maintenance of the bone graft bed, and fusion. Outcomes: At follow-up, the hardware was found to be in good condition, with no significant loss of cervical lordosis. At the 37-month follow-up after her second operation, the patient was doing better and continuing to recover. Lessons: We concluded that nonideal choice of occipitocervical angle may play an important role in rod breakage; however, an inadequate bone graft and poor postoperative fusion may also contribute to implant failure.