Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered Immune Reconstitution in Allogeneic Stem Cell Transplant Recipients With Human Immunodeficiency Virus (HIV)

Background. Persons living with human immunodeficiency virus (HIV) are at elevated risk of developing the malignant diseases that require allogeneic stem cell transplantation (ASCT). Recent data suggest that these individuals are also at an elevated risk of certain complications post-ASCT. This risk may result from preexisting HIV-related factors affecting dynamics of immune reconstitution post-ASCT. However, to date, there has been little work describing the dynamics of immune reconstitution post-ASCT in persons with HIV and none comparing these data to controls without HIV. Methods. We assessed T-cell reconstitution in 6 ASCT with HIV recipients (HIV+ASCT) compared to a control population of 21 ASCT without HIV recipients. In a subset of HIV+ASCT recipients we performed additional flow cytometry profiling of CD8+ T-cell subsets and antigen specificity of reconstituting CD4+ and CD8+ T cells. Results. We observe no difference in post-ASCT CD4+ T cells between HIV+ASCT and HIV-negative ASCT recipients, despite much lower pre-ASCT CD4+ T-cell counts in the HIV+ASCT group. In contrast, we observed significantly higher CD8+ T-cell numbers in the HIV+ASCT group post-ASCT. The reconstituting CD8+ T-cells were predominantly CD45RO+, whereas homing markers and antigen specificity of these cells varied between participants. Conclusion. This study represents the most extensive characterization of immune-reconstitution post-ASCT in persons with HIV, and the first to our knowledge to compare these data to ASCT controls without HIV. The results indicate that immune reconstitution in this group can be affected by preexisting HIV infection and post-ASCT antigen exposure.
Life-table representations of family dynamics in Sweden and Hungary: initiation of a project of descriptions of demographic behavior

In this paper, we present a system of descriptions of family-demographic behavior in developed countries. We use life-table techniques in order to describe the experiences of men, women, and children in processes related to family formation and family dissolution. We develop a large number of descriptive measures and apply them to survey data from Sweden and Hungary. The paper demonstrates the potential of our descriptive system for further cross-country comparisons of the demographic behavior in European countries. (AUTHORS)
Gender Differences in Chronic Exposure to Traffic-Related Air Pollution—A Simulation Study of Working Females and Males

The objective of this study was to identify spatial variability in exposure to outdoor traffic-related air pollution with specific emphasis on comparing exposure estimates for working females and males across a metropolitan area. A spatial exposure simulation model was used to estimate annual average exposure to traffic-related nitrogen dioxide for males and females reporting regular work in census tracts other than that of their residence, in Vancouver, British Columbia. The model produced estimates of annual average exposure in six microenvironments (home indoor, work indoor, other indoor, outdoor, in-vehicle to work, and in-vehicle other) using time-activity patterns and work flow data, for males and females in each of 382 census tracts. This allowed for the identification of spatial variations in exposure estimates for each gender, due to mobility within the study region. Indoor sources of nitrogen dioxide were not included in the simulation. No significant differences in estimated total exposure were found between working females and males in general. Small but observable spatial differences, however, were found between working females and males at the 90th percentile of the exposure distributions associated specifically with the work indoor microenvironment. These were highest in suburban areas (+3 μ g/m3 for females, relative to total exposures in the range of 26 to 37 μ g/m3 annual average hourly nitrogen dioxide). These results identify specific geographic locations in the study area where personal monitoring studies might be warranted and suggest that the inclusion of workplace locations in multivariate modeling could be useful to further understand differences in estimated exposures.
Gastrointestinal Tract Plasmablastic Lymphoma in HIV Infected Adults: A Histopathological Audit

Background: Plasmablastic lymphoma (PBL) is an aggressive B-cell lymphoma that is characterized by the expression of plasma cell antigens and loss of pan B-cell antigens. The neoplasm is extensively reported in the oral cavity and anorectal region but rarely in the gastrointestinal tract whereby isolated case reports and small case series exist. In the current study, the morphologic, immunohistochemical and molecular features of 17 cases of gastrointestinal tract PBL were reviewed. Materials and Methods: Ten-year retrospective study that reappraised the histomorphological and immunophenotypic features of HIV-associated PBL in the gastrointestinal tract those were diagnosed and coded as ‘plasmablastic lymphoma’. Results: The average age of the study subjects was 41 years with a 3:1 ratio of males to females. The most frequent site of involvement was the small intestine (42%). Majority of the cases showed a predominant diffuse (82%) and single cell (29%) growth patterns. Immunoblastic and plasmablastic cytomorphology was common in all cases. Sixty-five percent of the cases exhibited scattered centroblasts and one case demonstrated predominance of centroblasts. Other features observed include pseudoalveolar growth pattern, plasmacytic differentiation (25%cases), multinucleated giant cells, clear cell change, high mitotic activity with high proliferative indices (Ki-67 >90%), apoptosis (100% cases) and necrosis (71% cases). Immunohistochemistry revealed absence of pan B-cell antigens and expression of plasma cell antigens. Epstein-Barr virus-encoded RNA was expressed in 53% of the cases and one case showed c-MYC translocation. Conclusion: This study highlights the spectrum of histopathological features of gastrointestinal tract PBLs. Additional observations not previously described or emphasized in literature includes pseudo alveolar growth pattern, Centro blast-predominance, multinucleated giant cells and clear cell change. Awareness of the histopathological spectrum and immunohistochemical profile of gastrointestinal tract PBLs may aid in accurate diagnosis and avert potential diagnostic errors.
Report of EEG Finding on Critically Ill Patients with COVID-19

In March 2020, we treated a cohort of 26 critically ill hospitalized SARS-CoV-2 infected patients who received EEGs to assess unexplained altered mental status, loss of consciousness, or poor arousal and responsiveness. Of the 26 patients studied, 5 patients had EEGs that showed Periodic Discharges (PD) consisting of high amplitude frontal monomorphic delta waves with This article is protected by copyright. All rights reserved. absence of epileptic activity. These findings may suggest CNS injury potentially related to COVID-19 in these patients.
Comparative transcriptomics reveal conserved impacts of rearing density on immune 2 response of two important aquaculture species 3 4

19 Infectious diseases represent an important barrier to sustainable aquaculture development. 20 Rearing density can substantially impact fish productivity, health and welfare in aquaculture, 21 including growth rates, behaviour and, crucially, immune activity. Given the current emphasis 22 on aquaculture diversification, stress-related indicators broadly applicable across species are 23 needed. Utilising an interspecific comparative transcriptomic (RNAseq) approach, we 24 compared gill gene expression responses of Atlantic salmon (Salmo salar) and Nile tilapia 25 (Oreochromis niloticus) to rearing density and Saprolegnia parasitica infection. Salmon reared 26 at high-density showed increased expression of stress-related markers (e.g. c-fos and hsp70), 27 and downregulation of innate immune genes. Upon pathogen challenge, only salmon reared 28 at low density exhibited increased expression of inflammatory interleukins and lymphocyte29 related genes. Tilapia immunity, in contrast, was impaired at low-density. Using overlapping 30 gene ontology enrichment and gene ortholog analyses, we found that density-related stress 31 similarly impacted salmon and tilapia in key immune pathways, altering the expression of 32 genes vital to inflammatory and Th17 responses to pathogen challenge. Given the challenges 33 posed by ectoparasites and gill diseases in fish farms, this study underscores the importance 34 of optimal rearing densities for immunocompetence, particularly for mucosal immunity. Our 35 comparative transcriptomics analyses identified density stress impacted immune markers 36 common across different fish taxa, providing key molecular targets with potential for monitoring 37 and enhancing aquaculture resilience in a wide range of farmed species. 38
Modelling bioclimate by means of Fourier analysis of NOAA‐AVHRR NDVI time series in Western Argentina

This study assessed whether the relationship of climate with foliar phenology is sufficiently robust to use a measure of foliar phenology to interpolate climate statistics in areas where observations are sparse. The normalized difference vegetation index (NDVI) was used to represent vegetation activity. As a measure of foliar phenology, we used parameters obtained by modelling NDVI time series with a Fast Fourier Transform (FFT) applied to a 9‐year time series of monthly National Oceanographic and Atmospheric Administration (NOAA) advanced very high resolution radiometer (AVHRR) NDVI global area coverage (GAC) images. The FFT decomposes the series into an average signal and to sinusoidal components. The selected FFT parameters were mean NDVI, and amplitude and phase for a 1‐year period. Our specific objective was to relate the ratio of precipitation, P, over potential evapotranspiration, ETP, to the FFT parameters in two complementary ways. The first was to use them as attributes in a numerical classification to obtain a map of foliar isophenology, and then associate these classes with bioclimatic types, thus generating a bioclimatic map. The second was to fit a multiple linear regression model with P/ETP as predicted variable and the FFT parameters as predictive variables. The regression model was then applied to obtain a map of the ratio P/ETP. The latter gave a second bioclimatic map. Foliar isophenology classes show a north–south decrease in phase value and increase in amplitude and mean NDVI values, thus reflecting the transition in climate conditions from hotter and drier to wetter and cooler. The model explains 92% (p‐value < 10−12) of the spatial variation in the P/ETP ratio. When using a single FFT parameter, no significant relationship was obtained. The three parameters provide complementary information to understand phenological variability in response to climate variability. Modelling bioclimate by means of monthly NDVI series summarized by Fourier analysis is an adequate tool to extend climate data where they are sparse. Copyright © 2007 Royal Meteorological Society
L’évolution hydromorphologique de la vallée du Yamé (Pays Dogon, Mali) : signal climatique et hydrosystème continental en Afrique de l’Ouest entre 50 et 4 ka cal. BP

Le remplissage alluvial de la vallee du Yame incisee dans le plateau greseux de Bandiagara (Mali) a enregistre les reponses hydrologiques et geomorphologiques aux changements environnementaux des regions soudano-saheliennes durant les cinquante derniers millenaires. Des recherches de terrain et de laboratoire, avec respectivement 41 datations OSL et 88 datations radiocarbone, ont permis d’identifier sept sequences sedimentaires pleistocenes et dix-sept sequences holocenes sur le site d’Ounjougou. Des donnees paleoenvironnementales tirees d’etudes palynologiques et anthracologiques anterieures permettent d’etablir des correlations entre styles fluviaux et taux d’alluvionnement d’une part et changements climatiques et anthropiques dans le bassin versant d’autre part. Les resultats obtenus sont ensuite compares aux donnees paleoenvironnementales recentes disponibles en Afrique occidentale, des regions guineennes au Maghreb, ainsi qu’aux donnees issues des carottages marins ou lacustres, soulignant l’interet des sediments fluviatiles pour la comprehension des effets des fluctuations climatiques sur les environnements continentaux.
Methane Production in the Rumen and its Influence on Global Warming

In the last decades greenhouse gases emissions are a great concern globally. It is well known that from the agricultural sector, ruminant livestock due to natural fermentation process contributes substantially to the increase in methane production. Methane emissions represent the second contributors to global warming but it has a potential of 23 times more than carbon dioxide. Ruminal methanogenesis represents an energy loss to the animal besides contribution to greenhouse gases emissions. Many attempts have been initiated to reduce ruminal methane productions in an ecologically and sustainable way, such us: immunization against ruminal methanogenesis, defaunation, uses of chemicals additives, ionophore antibiotics, plant extracts or diet changes. This paper presents the methanogenesis process in rumen, its impact on climate change and a number of mitigation strategies that can be effective in vivo and in vitro .
ISOLATED SPERMATOZOA AS INDICATORS OF MUTATIONS TRANSMITTED TO PROGENY by MICHELLE BETH NORRIS

PROGENY by MICHELLE BETH NORRIS (Under the Direction of Richard N. Winn) ABSTRACT We used λ transgenic medaka to evaluate whether analysis of mutations directly in isolated spermatozoa is a reliable alternative to using progeny to assess genetic health risks. Mutant frequencies of cII targets (MF) in spermatozoa exposed to ethylnitrosurea (ENU) at either post-meiotic or pre-meiotic germ-cell stages of spermatogenesis were compared. The MFs of exposed pre-meiotic stem cell spermatogonia showed a significant 9-fold induction in MF, consistent with progeny analyses. By contrast, significantly elevated MFs were detected in progeny derived from ENU-treated post-meiotic germ cells, but not in isolated spermatozoa. DNA damage not fixed as a cII mutation in spermatozoa will not be detected. However, damage in spermatozoa that persists to or after fertilization can be fixed as a mutation and is detected in the embryo. Consequently, using isolated spermatozoa can provide a reliable alternative to using progeny providing the spermatozoa sampled correspond to pre-meiotic germ-cell stages exposed to the mutagen.
Adopting a New Religion: The Case of Protestantism in 16th Century Germany

Using a rich dataset of territories and cities of the Holy Roman Empire in the 16th century, this paper investigates the determinants of adoption and diffusion of Protestantism as a state religion. A territory’s distance to Wittenberg, the city where Martin Luther taught, is a major determinant of adoption. This finding can be explained through a theory of strategic neighbourhood interactions: in an uncertain legal context, introducing the Reformation was a risky enterprise for territorial lords, and had higher prospects of success if powerful neighbouring states committed to the new faith first. The model is tested in a panel dataset featuring the dates of introduction of the Reformation.
Science-Based Dating in Archaeology

Part 1 Generalities: the impact of scientific techniques absolute dating and derivative dating the event being dated reasons for dating which technique? dating terminology. Part 2 Climatic clocks and frameworks: climate-based frameworks the oxygen-isotope timescale - the Milankovitch astronomical theory of climate the pollen record (palynology) - late-glacial and postglacial dating in NW Europe, pollen assemblage zones (PAZ), correlation with the oxygen-isotope timescale - La Grand Pile, Les Echets varve chronology - the Scandianavian varbe chronology, the Lake of Clouds, Minnesota dendrochronology (tree-ring dating - the European oak and bristlecone pine chronology. Part 3 Radiocarbon dating: the essential basis the carbon exchange reservoir concentration ration variations - past millennia recent, man-made disturbances other cosmogenic isotopes - calcium -41 the two approaches - beta activity and atom counting - accelerator mass spectrometry (AMS) effect of contamination samples and sampling - wood, bone, shell, sediments and soild, peat, mortar, stalagmites etc step towards a calendar date beyond calibration. Part 5 Potassium-argon, uranium-series, fission tracts. Part 6 Luminescence dating: thermoluminescence (TL) paleodose and annual dose on-site procedures laboratory measurements - Alpha counting, Beta TLD, alkali feldspar - the isochron technique, zircon dating accuracy and error limits, date citation, age range authenticity testing beyond pottery - burnt flint, burnt stones, unburnt materials - calcite, shell, bone and teeth optical dating - dating of mineral fractions from Viking pottery fragments, dating of the church of Santa maria Foris Portas, Lombardy, Italy. Part 7 Electron spin resonance (ESR): radioactivity and annual dose applications - stalagmitic calcite, travertine, tooth enamel. Part 8 Amino acid racemization, obsidian hydration, other chemical methods. Part 9 Magnetic dating and magnetostratigraphy: the Earth's magnetic field recording mechanisms - thermoremanent magnetism (TRM)k viscous remanent magnetism (VRM), sediments (DRM, PDRM CRM) sampling and measurement the magnetic polarity timescale (reversal stratigraphy) archaeomagnetism - the Fisher index.
Applying Receptor Models To Analyze Urban/Suburban VOCs Air Quality in Martorell (Spain)

Airborne concentrations of several VOCs were measured in the city of Martorell (Spain) and analyzed by using a receptor modeling approach in order to assess the contribution of several potential sources of VOCs. In addition, VOC concentrations in Martorell are compared to VOC levels in 16 other cities of the world. Special attention throughout the paper is focused on the comparison between results obtained with data from an urban environment and data from a suburban area. Compared to the other cities, VOCs air quality in Martorell do not stand out for being neither among the worst nor among the best. The goal of setting relationships between airborne concentrations and pol lutant sources is approached by a principal component analysis coupled to multiple linear regression. These procedures allow one to identify sources of VOCs pollution. A subsequent multiple linear regression allows us to estimate emission profiles for significant sources. The main source of VOCs pollution in Martorell is road traffic, c.
17β‐Estradiol: a novel hormone for improving immune and cardiovascular responses following trauma‐hemorrhage

17β‐Estradiol (i.e., estrogen or E2) is a female sex steroid, which plays an essential role in female reproductive physiology. However, several lines of evidence indicate that in addition to its role in reproductive physiology, E2 is critical for maintaining many other organ functions in stress conditions. These include immune, cardiovascular, and neuronal functions, as well as regulation of skin, bone, and lipid metabolism. Studies have examined the role of E2 as an adjunct in post‐trauma responses, and this article will review whether E2 as an adjunct to fluid resuscitation following trauma‐hemorrhage plays any role in improving/restoring immune and cardiovascular functions.
A Web-Based Cognitive Behavioral Therapy, Mindfulness Meditation, and Yoga Intervention for Posttraumatic Stress Disorder: Single-Arm Experimental Clinical Trial

Background: Posttraumatic stress disorder (PTSD) is a debilitating, undertreated condition. The web-based delivery of cognitive behavioral therapy supplemented with mindfulness meditation and yoga is a viable treatment that emphasizes self-directed daily practice. Objective: This study aims to examine the effectiveness of a web-based cognitive behavioral therapy, mindfulness, and yoga (CBT-MY) program designed for daily use. Methods: We conducted an 8-week, single-arm, experimental, registered clinical trial on adults reporting PTSD symptoms (n=22; aged 18-35 years). Each participant received web-based CBT-MY content and an hour of web-based counseling each week. Pre-post outcomes included self-reported PTSD symptom severity, depression, anxiety, chronic pain, and mindfulness. Pre-post psychophysiological outcomes included peak pupil dilation (PPD) and heart rate variability (HRV). HRV and PPD were also compared with cross-sectional data from a non-PTSD comparison group without a history of clinical mental health diagnoses and CBT-MY exposure (n=46). Results: Pre-post intention-to-treat analyses revealed substantial improvements in PTSD severity ( d =1.60), depression ( d =0.83), anxiety ( d =0.99), and mindfulness ( d =0.88). Linear multilevel mixed models demonstrated a significant pre-post reduction in PPD ( B= −0.06; SE=0.01; P <.001; d =0.90) but no significant pre-post change in HRV ( P =.87). Overall, participants spent an average of 11.53 (SD 22.76) min/day on self-directed mindfulness practice. Conclusions: Web-based CBT-MY was associated with clinically significant symptom reductions and significant PPD changes, suggesting healthier autonomic functioning. Future randomized controlled trials are needed to further examine the gains apparent in this single-arm study.
Sparse Coding Driven Deep Decision Tree Ensembles for Nuclear Segmentation in Digital Pathology Images

In this paper, we propose an easily trained yet powerful representation learning approach with performance highly competitive to deep neural networks in a digital pathology image segmentation task. The method, called sparse coding driven deep decision tree ensembles that we abbreviate as ScD2TE, provides a new perspective on representation learning. We explore the possibility of stacking several layers based on non-differentiable pairwise modules and generate a densely concatenated architecture holding the characteristics of feature map reuse and end-to-end dense learning. Under this architecture, fast convolutional sparse coding is used to extract multi-level features from the output of each layer. In this way, rich image appearance models together with more contextual information are integrated by learning a series of decision tree ensembles. The appearance and the high-level context features of all the previous layers are seamlessly combined by concatenating them to feed-forward as input, which in turn makes the outputs of subsequent layers more accurate and the whole model efficient to train. Compared with deep neural networks, our proposed ScD2TE does not require back-propagation computation and depends on less hyper-parameters. ScD2TE is able to achieve a fast end-to-end pixel-wise training in a layer-wise manner. We demonstrated the superiority of our segmentation technique by evaluating it on the multi-disease state and multi-organ dataset where consistently higher performances were obtained for comparison against several state-of-the-art deep learning methods such as convolutional neural networks (CNN), fully convolutional networks (FCN), etc.