Miracle-dz/UniFAR-FTUs huggingface dataset:
Virus Neutralizing Antibodies Detectable in Survivors of Outbreak 40 Years after

The first reported outbreak of Ebola virus disease occurred in 1976 in Yambuku, Democratic Republic of Congo. Antibody responses in survivors 11 years after infection have been documented. However, this report is the first characterization of anti-Ebola virus antibody persistence and neutralization capacity 40 years after infection. Using ELISAs we measured survivor’s immunological response to Ebola virus Zaire (EBOV) glycoprotein and nucleoprotein, and assessed VP40 reactivity. Neutralization of EBOV was measured using a pseudovirus approach and plaque reduction neutralization test with live EBOV. Some survivors from the original EBOV outbreak still harbor antibodies against all 3 measures. Interestingly, a subset of these survivors’ serum antibodies could still neutralize live virus 40 years postinitial infection. These data provide the longest documentation of both anti-Ebola serological response and neutralization capacity within any survivor cohort, extending the known duration of response from 11 years postinfection to at least 40 years after symptomatic infection.
Matrix Degradation in Human Immunodeficiency Virus Type 1–Associated Tuberculosis and Tuberculosis Immune Reconstitution Inflammatory Syndrome: A Prospective Observational Study

Walker, Naomi F; Wilkinson, Katalin A; Meintjes, Graeme; Tezera, Liku B; Goliath, Rene; Peyper, Janique M; Tadokera, Rebecca; Opondo, Charles; Coussens, Anna K; Wilkinson, Robert J; +2 more. Friedland, Jon S; Elkington, Paul T; (2017) Matrix Degradation in Human Immunodeficiency Virus Type 1-Associated Tuberculosis and Tuberculosis Immune Reconstitution Inflammatory Syndrome: A Prospective Observational Study. Clinical infectious diseases, 65 (1). pp. 121-132. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/cix231 Downloaded from: http://researchonline.lshtm. ac.uk/id/eprint/3911130/
Sensitivity

Substance use disorder (SUD) affects approximately 100 million people worldwide (Orford et al., 2012), with approximately 27 million in the US (Substance Abuse and Mental Health Services Administration, 2016a). Worldwide, mortality rates are 33.0 (alcohol) and 6.9 (drugs) deaths per 100 000, and rising (Peacock et al., 2017). As a single cause for addiction is yet to be identified, a single successful treatment modality is also unknown. Various approaches are used including medication, counselling, and mutual-help groups. While the efficacy of current treatment methods for SUD remains inconclusive, the cost is considerable.
Electronic Supplementary Material for : A mathematical model of cocoa bean fermentation Journal of Royal Society – Open Science

a midpoint from the above ranges can be computed in order to determine a theoretical volume for a single cell, where a is equal to the length minus two times the radius (r). Thus, for lactic acid bacteria (LAB) the volume is equal to 4.46 μm3 and for acetic acid bacteria (AAB) it is ≈ 1 μm3. Therefore; using as reference the dry weight of a single cell of E. coli reported by Neidhardt & Umbarger [3] of 2.8× 10−10 mg and its volume of 1 μm3 [4], the conversion factor between CFU to dry biomass of LAB and AAB were determined as 1.25 and 0.28 pg CFU−1 respectively.
Introducing litter quality to the ecosystem model LPJ-GUESS: Effects on short- and long-term soil carbon dynamics

Many biogeochemical models have been applied to study the response of the carbon cycle to changes in climate, whereby the process of carbon uptake (photosynthesis) has usually gained more attention than the equally important process of carbon release by respiration. The decomposition of soil organic matter is driven by a combination of factors like soil temperature, soil moisture and litter quality. We have introduced dependence on litter substrate quality to heterotrophic soil respiration in the ecosystem model LPJ-GUESS [Smith et al.(2001)]. We were interested in differences in model projections before and after the inclusion of the dependency both in respect to shortand long-term soil carbon dynamics.
Interleukin-6 Promoter Haplotypes and Interleukin-6 Cytokine Responses

Genetic variations contribute to differences in the inflammatory response and are markers for disease risk and outcomes. We studied three single-nucleotide polymorphisms (−597 G→A, −572 G→C, and −174 G→C) in the IL-6 promoter to determine associations with ex vivo LPS-stimulated IL-6 production by leukocytes. We also measured nuclear protein binding to synthetic oligonucleotides representing the −174 polymorphic region, located in proximity to important transcription factor motifs. We determined genotypes at three sites in the IL-6 promoter by pyrosequencing of genomic DNA obtained from 49 healthy control subjects. To determine molecular haplotypes, cloned DNA fragments from heterozygous subjects were sequenced. IL-6 release by whole blood leukocytes was measured after 24 h of ex vivo LPS stimulation. We compared IL-6 concentrations between haplotypes using Kruskall-Wallis and adjusted for covariates by analysis of covariance. Electromobility gel shift assay was carried out by the incubation of nuclear proteins from cultured human mononuclear cells with oligonucleotides representing the alternate −174 alleles. The amount of nuclear protein binding was quantified by densitometry, which was compared using analysis of variance. Genotype and sequence analysis of genomic and cloned DNA characterized three haplotypes. Ex vivo IL-6 production was greatest in individuals who were homozygous for the haplotype containing guanine at −597 and −174. IL-6 production was least for individuals homozygous for the haplotype containing adenine at −597 and cytosine at −174. Nuclear protein bound more avidly to guanine-containing oligonucleotides representing the −174 position than to oligonucleotides containing cytosine at that position. The IL-6 promoter haplotype influences ex vivo IL-6 response to endotoxin. This effect may be due to a functional effect of the –174 G→C polymorphism.
The effect of positive changes during intraoperative monitoring of the functional improvement in patients with cervical compressive myelopathy

Background: Cervical compressive myelopathy (CCM) is a progressive, degenerative spine disease and the most common cause of spinal cord dysfunction in older individuals. Current clinical guidelines for spinal surgery recommend multimodal intraoperative monitoring (IOM) during spinal surgery as a reliable and valid diagnostic adjunct to assess spinal cord integrity. The aim of this study was to evaluate the effect of positive changes during IOM on the functional status in patients with CCM. Methods: Patients who underwent spinal surgery with IOM due to CCM were enrolled. During the surgery, patients underwent IOM using motor evoked potential (MEP) and somatosensory evoked potential (SEP). MEP and SEP were checked before and immediately after decompression. A decrease in latency . 10% or an increase in amplitude . 50% was regarded as a “positive changes”. Subjects were divided according to the presence of positive changes. Motor scores of American Spinal Injury Association (ASIA) impairment scale and Korean version of Modified Barthel Index (K-MBI) were evaluated before and after operation. Results: Twenty-nine patients underwent spinal surgery due to CCM. Eleven patients showed positive changes in MEP during IOM. When the two groups were compared, improvement rate in the ASIA motor score and K-MBI were significantly higher in patients with positive changes than in patients without positive changes at 1 month after surgery. However, 6 months after surgery, there were no significance differences between the groups. Regardless of positive change, nearly all patients suffered from neuropathic pain after operation. Conclusion: Positive changes in MEP during IOM may affect functional improvement 1 month after operation and early discharge without significant complications in CCM patients. However, they do not affect the neuropathic pain and long-term functional outcome. Thus, tailored proper management is needed to achieve maximal functional recovery in each patient after cervical spinal decompression surgery.
Molecular epidemiology of coagulase-negative Staphylococcus carriage in 1 neonates admitted to an intensive care unit in Brazil 2

18 Background 19 Nasal colonization with coagulase-negative Staphylococcus (CoNS) has been 20 described as a risk factor for subsequent systemic infection. In this study, we aimed to 21 evaluate the profile of CoNS isolates colonizing the nares of children admitt e to a 22 neonatal intensive care unit (NICU) of a major city located in central Braz il. 23 Methods 24 We assessed CoNS carriage at admittance and discharge among newborns admi tted to 25 an NICU from July 2007 through May 2008 in one of the major municipalities of 26 Brazil. Isolates were screened on mannitol salt agar and tryptic soy broth an d tested 27
A multicenter, prospective, randomized study protocol to demonstrate the superiority of a bone-anchored prosthesis for anular closure used in conjunction with limited discectomy to limited discectomy alone for primary lumbar disc herniation

Background: Same-level reherniation and progressive degeneration with disc height loss are main causes of poor outcome after discectomy and may necessitate reoperation. A novel prosthesis for anular closure was developed to address these causes. Methods: The design of a multicenter, prospective, randomized, post-market superiority trial comparing limited lumbar discectomy augmented with this device (intervention group) with limited lumbar discectomy alone (control group) is presented. Results: Patients with single-level (L1-S1) posterior or posterolateral disc herniation and radiologic confirmation of neural compression for whom at least six weeks of conservative treatment has failed are eligible. Patients must have posterior disc height ≥5 mm at index level and baseline Oswestry and VAS leg pain scores of ≥40/100. Intraoperatively, subjects meeting anular defect size criteria post-discectomy (4-6 mm tall and 6-10 mm wide) will be randomized to study groups in a 1:1 ratio using centralized, web-based software. A Bayesian statistical approach will be used to enroll 400 to 800 subjects who will be followed for at least 24 months. Two co-primary endpoints will be assessed at 24 months: 1) a composite of leg pain, clinical function, disc height maintenance, and absence of reherniation, reoperation, and device failure; and 2) absence of reherniation based upon independent radiologic analysis. Conclusions: This type of analysis is becoming increasingly important as governments and health insurers continue to be pressured to spend limited healthcare funding wisely.
Morphometrical evaluation of the choriocapillaris imaged by swept-source optical coherence tomography angiography

Purpose: To assess the reproducibility of quantitative morphometrical evaluation of the choriocapillaris imaged with swept-source optical coherence tomography angiography (SS-OCTA). Subjects and methods: This observational, cross-sectional case series included 35 eyes of healthy individuals and 32 eyes of 32 patients. Two images of the fovea were taken using SS-OCTA with 3 × 3 mm squares. Images of the choriocapillaris within 800 × 800 pixel squares centered at the fovea were analyzed morphometrically using open-source software “AngioTool” that applies a Gaussian recursive filter and multiscale Hessian enhancement. This program’s vessel thickness and intensity parameters can be changed to aid vessel detection. We measured the pairs of images per eye with different parameter sets and calculated the intraclass correlation (ICC) for the morphometrical results. After determining the parameters that produced high reproducibility, we evaluated regional variations in 800 × 800 pixel mm squares within the fovea. Results: The ICCs for vessel area, total vessel length, vessel diameter index, and mean lacunarity were over 0.9 using the parameters of “vessel thickness” 3–4 and intensity 15 in the group including all subjects. When measurements were performed using these same parameter values, the vessel density and mean vessel diameter index were 60.5% and 19.1 ± 0.389, respectively. Vessel density, vessel length, vessel diameter index, and mean lacunarity did not change significantly within an 800 × 800 pixel square centered at the fovea except for the 200 × 200 pixel square at the foveal center. Conclusion: SS-OCTA images of the choriocapillaris can be measured with high reproducibility by morphometrical evaluation using open-source software with multiscale Hessian enhancement. Such automated morphometric analysis can provide an objective evaluation of the choriocapillaris.
Unsupervised Deep Change Vector Analysis for Multiple-Change Detection in VHR Images

Change detection (CD) in multitemporal images is an important application of remote sensing. Recent technological evolution provided very high spatial resolution (VHR) multitemporal optical satellite images showing high spatial correlation among pixels and requiring an effective modeling of spatial context to accurately capture change information. Here, we propose a novel unsupervised context-sensitive framework—deep change vector analysis (DCVA)—for CD in multitemporal VHR images that exploit convolutional neural network (CNN) features. To have an unsupervised system, DCVA starts from a suboptimal pretrained multilayered CNN for obtaining deep features that can model spatial relationship among neighboring pixels and thus complex objects. An automatic feature selection strategy is employed layerwise to select features emphasizing both high and low prior probability change information. Selected features from multiple layers are combined into a deep feature hypervector providing a multiscale scene representation. The use of the same pretrained CNN for semantic segmentation of single images enables us to obtain coherent multitemporal deep feature hypervectors that can be compared pixelwise to obtain deep change vectors that also model spatial context information. Deep change vectors are analyzed based on their magnitude to identify changed pixels. Then, deep change vectors corresponding to identified changed pixels are binarized to obtain a compressed binary deep change vectors that preserve information about the direction (kind) of change. Changed pixels are analyzed for multiple CD based on the binary features, thus implicitly using the spatial information. Experimental results on multitemporal data sets of Worldview-2, Pleiades, and Quickbird images confirm the effectiveness of the proposed method.
Understanding the Structure and Function of the Immunological Synapse

References http://cshperspectives.cshlp. org/content/2/10/a002311.full. html#ref-list-1 This article cites 99 articles, 36 of which can be accessed free service Email alerting click here box at the top right corner of the article or Receive free email alerts when new articles cite this article sign up in the Subject collections (14 articles) Immunoreceptor Signaling  Articles on similar topics can be found in the following collections
Heidelberg-mCT-Analyzer : a novel method for standardized micro-computed-tomography-( mCT )-guided evaluation of scaffold properties in bone and tissue research

Aims Bone tissue engineering and the development of optimum bone scaffolds represent two of the most challenging fields in orthopedic research and have a high clinical relevance (1, 2). For the non-invasive characterization and evaluation of scaffold properties and their biological behavior, micro-computed-tomography (mCT) is a reliable and appropriate tool, because it measures microstructures directly without depending on stereologic models (3). Especially porosity (P), pore volume (PV), and surface structure (SS) seem to be crucial parameters characterizing the properties of scaffolds that increase bone healing and regeneration (4). Particularly mCT analysis is capable of investigating common scaffold parameters (Table 1), so mCT seems to be a reliable tool for the non-invasive analysis of scaffold structure (5).
Molecular and Serologic Characterization, Pathogenicity, and Protection Studies with Infectious Bronchitis Virus Field Isolates from California

Abstract In this study, we characterized three variant infectious bronchitis virus (IBV) strains isolated in 2003 and 2004 from broiler chickens in California and compared them to previously isolated California variant viruses and to common vaccine serotypes used in the United States. We conducted genetic, serologic, and pathogenicity studies on all three isolates, then tested different vaccines against one of the viruses. Genetically the three variant IBV strains, designated CA557/03, CA706/03, and CA1737/04, were not related to each other. GenBank BLAST database search and phylogenetic analysis of the hypervariable region of the S1 subunit of the spike gene to determine the most closely related viruses to the three variants showed the CA557/03 variant to be 81.8% similar to the CAV/CA56b/91 whereas the CA706/03 and CA1737/04 variant viruses were only distantly related to Dutch/D1466/81 (72.2%), a vaccine strain used in Europe, and Korea/K142/02 (72.7%), a Korean field isolate, respectively. Cross virus-neutralization testing showed that none of the 2003–04 California IBV variant viruses were serologically related to each other or to Ark, Conn, or Mass vaccine strains. In addition the CA1737/04 isolate was also tested against DE072 and found not to be serologically related. All three variant viruses were pathogenic in 1-wk-old broilers and vaccination with Mass/Conn followed by Holland/Conn provided 80% protection against the CA1737/04 virus. The 2003–04 California variant viruses were not compared with variants isolated in California during 1970s and 1980s because, to our knowledge, no genetic information is available and those viruses are no longer obtainable. This study shows that the CA557/03 virus was distantly related to the CAV-type viruses isolated in California in the early 1990s, but that none of the 2003–04 viruses were similar genetically or serologically to the CAL99-type viruses, indicating that new IBV variants continue to emerge and cause disease in commercial chickens in California.
Complex role of HiF in cancer: the known, the unknown, and the unexpected

: Tumor hypoxia has long been recognized as a driving force of malignant progression and therapeutic resistance. The discovery of hypoxia-inducible transcription factors (HIFs) has greatly advanced our understanding of how cancer cells cope with hypoxic stress by maintaining bioenergetics through the stimulation of glycolysis. Until recently, however, it remained perplex-ing why proliferative cancer cells opt for aerobic glycolysis, an energy-inefficient process of glucose metabolism. Furthermore, the role of HIF in cancer has also become complex. In this review, we highlight recent groundbreaking findings in cancer metabolism, put forward plausible explanations to the complex role of HIF, and underscore remaining issues in cancer biology.
Tailoring mathematical models to stem-cell derived cardiomyocyte lines can improve predictions of drug-induced changes to their electrophysiology. Frontiers

to Stem-Cell Derived Lines Can Improve Predictions Human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs) have applications in disease modeling, cell therapy, drug screening and personalized medicine. Computational models can be used to interpret experimental ﬁndings in iPSC-CMs, provide mechanistic insights, and translate these ﬁndings to adult cardiomyocyte (CM) electrophysiology. However, different cell lines display different expression of ion channels, pumps and receptors, and show differences in electrophysiology. In this exploratory study, we use a mathematical model based on iPSC-CMs from Cellular Dynamic International (CDI, iCell), and compare its predictions to novel experimental recordings made with the Axiogenesis Cor.4U line. We show that tailoring this model to the speciﬁc cell line, even using limited data and a relatively simple approach, leads to improved predictions of baseline behavior and response to drugs. This demonstrates the need and the feasibility to tailor models to individual cell lines, although a more reﬁned approach will be needed to characterize individual currents, address differences in ion current kinetics, and further improve these results. These maximum conductances were then used to tailor the Paci et al. (2013) model to create cell-speciﬁc models of 22 diﬀerent Cor.4U cells. Using these tailored models to simulate APs, we found a variety of AP waveforms exhibiting a high level of variability similar to that found in real iPSC-CMs. We then optically measured action potential durations (APDs) in iPSC-CM cultures under both control and drug-applied conditions, and found that—in most cases—tailored models predicted the resulting changes better than the original model. This suggests that the ion current composition diﬀers between cell lines, and highlights the need to tailor in silico models to diﬀerent cell lines to interpret drug-induced alterations to their electrophysiology. Our results also show that even a relatively simple approach, in which only the maximum conductances are considered with limited experimental data, can already provide useful information in this regard, but that more intricate methods will be needed to characterize diﬀerences in outward currents between iPSC-CM cell lines.
ABCA7 frameshift deletion associated with Alzheimer disease in African Americans

Objective: To identify a causative variant(s) that may contribute to Alzheimer disease (AD) in African Americans (AA) in the ATP-binding cassette, subfamily A (ABC1), member 7 (ABCA7) gene, a known risk factor for late-onset AD. Methods: Custom capture sequencing was performed on ∼150 kb encompassing ABCA7 in 40 AA cases and 37 AA controls carrying the AA risk allele (rs115550680). Association testing was performed for an ABCA7 deletion identified in large AA data sets (discovery n = 1,068; replication n = 1,749) and whole exome sequencing of Caribbean Hispanic (CH) AD families. Results: A 44-base pair deletion (rs142076058) was identified in all 77 risk genotype carriers, which shows that the deletion is in high linkage disequilibrium with the risk allele. The deletion was assessed in a large data set (531 cases and 527 controls) and, after adjustments for age, sex, and APOE status, was significantly associated with disease (p = 0.0002, odds ratio [OR] = 2.13 [95% confidence interval (CI): 1.42–3.20]). An independent data set replicated the association (447 cases and 880 controls, p = 0.0117, OR = 1.65 [95% CI: 1.12–2.44]), and joint analysis increased the significance (p = 1.414 × 10−5, OR = 1.81 [95% CI: 1.38–2.37]). The deletion is common in AA cases (15.2%) and AA controls (9.74%), but in only 0.12% of our non-Hispanic white cohort. Whole exome sequencing of multiplex, CH families identified the deletion cosegregating with disease in a large sibship. The deleted allele produces a stable, detectable RNA strand and is predicted to result in a frameshift mutation (p.Arg578Alafs) that could interfere with protein function. Conclusions: This common ABCA7 deletion could represent an ethnic-specific pathogenic alteration in AD.