Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and Characterization of Adenoviruses Persistently Shed from the Gastrointestinal Tract of Non-Human Primates

Adenoviruses are important human pathogens that have been developed as vectors for gene therapies and genetic vaccines. Previous studies indicated that human infections with adenoviruses are self-limiting in immunocompetent hosts with evidence of some persistence in adenoid tissue. We sought to better understand the natural history of adenovirus infections in various non-human primates and discovered that healthy populations of great apes (chimpanzees, bonobos, gorillas, and orangutans) and macaques shed substantial quantities of infectious adenoviruses in stool. Shedding in stools from asymptomatic humans was found to be much less frequent, comparable to frequencies reported before. We purified and fully sequenced 30 novel adenoviruses from apes and 3 novel adenoviruses from macaques. Analyses of the new ape adenovirus sequences (as well as the 4 chimpanzee adenovirus sequences we have previously reported) together with 22 complete adenovirus genomes available from GenBank revealed that (a) the ape adenoviruses could clearly be classified into species corresponding to human adenovirus species B, C, and E, (b) there was evidence for intraspecies recombination between adenoviruses, and (c) the high degree of phylogenetic relatedness of adenoviruses across their various primate hosts provided evidence for cross species transmission events to have occurred in the natural history of B and E viruses. The high degree of asymptomatic shedding of live adenovirus in non-human primates and evidence for zoonotic transmissions warrants caution for primate handling and housing. Furthermore, the presence of persistent and/or latent adenovirus infections in the gut should be considered in the design and interpretation of human and non-human primate studies with adenovirus vectors.
Glucocorticoid Receptors on Alzheimer's Disease Mononuclear Leukocytes in

Several lines of evidence suggest disturbances of the hypothalamic- pituitary-adrenal (HPA) system in Alzheimer's disease (AD). In an exploration of the potential role of the glucocorticoid receptor (GR) in AD, GR density and affinity were assessed on mononuclear leukocytes of 12 AD patients and 12 healthy controls. GR binding characteristics did not differ between patients and controls or between patients subdivided according to diagnosis or associated clinical features. These data suggest that the abnormalities of the HPA system in AD are not related to a GR deficiency.
Changing HIV treatment eligibility under health system constraints in sub-Saharan Africa: investment needs, population health gains, and cost-effectiveness

Objective:We estimated the investment needs, population health gains, and cost-effectiveness of different policy options for scaling-up prevention and treatment of HIV in the 10 countries that currently comprise 80% of all people living with HIV in sub-Saharan Africa (Ethiopia, Kenya, Malawi, Mozambique, Nigeria, South Africa, Tanzania, Uganda, Zambia, and Zimbabwe). Design:We adapted the established STDSIM model to capture the health system dynamics: demand-side and supply-side constraints in the delivery of antiretroviral treatment (ART). Methods:We compared different scenarios of supply-side (i.e. health system capacity) and demand-side (i.e. health seeking behavior) constraints, and determined the impact of changing guidelines to ART eligibility at any CD4+ cell count within these constraints. Results:Continuing current scale-up would require US$178 billion by 2050. Changing guidelines to ART at any CD4+ cell count is cost-effective under all constraints tested in the model, especially in demand-side constrained health systems because earlier initiation prevents loss-to-follow-up of patients not yet eligible. Changing guidelines under current demand-side constraints would avert 1.8 million infections at US$208 per life-year saved. Conclusion:Treatment eligibility at any CD4+ cell count would be cost-effective, even under health system constraints. Excessive loss-to-follow-up and mortality in patients not eligible for treatment can be avoided by changing guidelines in demand-side constrained systems. The financial obligation for sustaining the AIDS response in sub-Saharan Africa over the next 35 years is substantial and requires strong, long-term commitment of policy-makers and donors to continue to allocate substantial parts of their budgets.
Influence of different tripeptides on the stability of the collagen triple helix. II. An experimental approach with appropriate variations of a trimer model oligotripeptide

A collagen model peptide comprising three covalently cross‐linked chains (Ala‐Gly‐Pro)8 with a stable triple‐helix conformation was utilized as the constant part of elongated model peptides of different composition. The tripeptides Gly‐Pro‐Hyp, Gly‐Pro‐Ala, Gly‐Pro‐Pro, Gly‐Pro‐Ser, Gly‐Ala‐Hyp, Gly‐Phe‐Hyp, Gly‐Glu‐Hyp, Gly‐Ala‐Lys, and Gly‐Pro‐Phe were coupled at the N‐terminal to the cross‐linked peptide. The transition temperatures determined by CD measurements are higher for the peptides containing the Gly‐X‐Hyp sequences followed by those with the Gly‐Pro‐Y sequences. In experiments with combinations of two different tripeptides coupled to the constant part of the cross‐linked model peptides higher transition temperatures were observed if the sequence of helix‐promoting tripeptides was not interrupted.
Millimeter-wave 14dBm CMOS power amplifier with input-output distributed transformers

We present a novel fully differential input/output distributed transformer topology used for the design of millimeter-wave power amplifiers. Input/output distributed transformers are used to feed the input signal to four differential couples and to combine their output power. This topology improves the stability and the efficiency of the power amplifier, minimizing the chip area. The PA prototype realized in a standard 65nm CMOS technology, supplied with 1.2V, achieves a 1dB single-ended output power compression point of 14dBm at 56GHz with a PAE of 8.3%, occupying only 0.2mm2.
Recent Tropical Expansion: Natural Variability or Forced Response?

Previous studies have documented a poleward shift in the subsiding branches of Earth’s Hadley circulation since 1979 but have disagreed on the causes of these observed changes and the ability of global climate models to capture them. This synthesis paper reexamines a number of contradictory claims in the past literature and finds that the tropical expansion indicated by modern reanalyses is within the bounds of models’ historical simulations for the period 1979–2005. Earlier conclusions that models were underestimating the observed trends relied on defining the Hadley circulation using the mass streamfunction from older reanalyses. The recent observed tropical expansion has similar magnitudes in the annual mean in the Northern Hemisphere (NH) and Southern Hemisphere (SH), but models suggest that the factors driving the expansion differ between the hemispheres. In the SH, increasing greenhouse gases (GHGs) and stratospheric ozone depletion contributed to tropical expansion over the late twentieth century, and if GHGs continue increasing, the SH tropical edge is projected to shift further poleward over the twenty-first century, even as stratospheric ozone concentrations recover. In the NH, the contribution of GHGs to tropical expansion is much smaller and will remain difficult to detect in a background of large natural variability, even by the end of the twenty-first century. To explain similar recent tropical expansion rates in the two hemispheres, natural variability must be taken into account. Recent coupled atmosphere–ocean variability, including the Pacific decadal oscillation, has contributed to tropical expansion. However, in models forced with observed sea surface temperatures, tropical expansion rates still vary widely because of internal atmospheric variability.
Retrospective Diagnosis of Pallister-Killian Syndrome by CGH Array

Objective and Methods: We report a girl presenting with a polymalformation syndrome. Despite a normal karyotype on peripheral lymphocytes and the unavailability of cultured fibroblasts, a tetrasomy 12p was identified on pulmonary DNA extracted from a postmortem biopsy, by use of comparative genomic hybridization (CGH) and confirmed by CGH array. The clinical picture of our patient was consistent, but not specific of the diagnosis of Pallister-Killian syndrome. She presented with the association of antenatal polyhydramnios, craniofacial dysmorphic features, skeletal abnormalities, and a congenital cardiopathy. Conclusion: We discuss the usefulness of CGH and CGH array in prenatal and constitutional cytogenetics.
Tuning ice nucleation with counterions on polyelectrolyte brush surfaces

This work is the first to show that the ion specificity in tuning HIN on ionic surfaces follows the Hofmeister series. Heterogeneous ice nucleation (HIN) on ionic surfaces is ubiquitous in a wide range of atmospheric aerosols and at biological interfaces. Despite its great importance in cirrus cloud formation and cryopreservation of cells, organs, and tissues, it remains unclear whether the ion-specific effect on ice nucleation exists. Benefiting from the fact that ions at the polyelectrolyte brush (PB)/water interface can be reversibly exchanged, we report the effect of ions on HIN on the PB surface, and we discover that the distinct efficiency of ions in tuning HIN follows the Hofmeister series. Moreover, a large HIN temperature window of up to 7.8°C is demonstrated. By establishing a correlation between the fraction of ice-like water molecules and the kinetics of structural transformation from liquid- to ice-like water molecules at the PB/water interface with different counterions, we show that our molecular dynamics simulation analysis is consistent with the experimental observation of the ion-specific effect on HIN.
Bmc Complementary and Alternative Medicine Justification for the Use of Ocimum Gratissimum L in Herbal Medicine and Its Interaction with Disc Antibiotics

Background: The ethanolic extract of the leaves of Ocimium gratisimum L. (Lamiaceae), used in traditional medicine for the treatment of several ailments such as urinary tract, wound, skin and gastrointestinal infections, was evaluated for its antibacterial properties against four clinical bacteria isolates namely: Escherichia coli, Proteus mirabilis, Staphylococcus aureus and Pseudomonas aeruginosa and the antifungal properties using a clinical isolate of Candida albicans. A typed bacterium of Escherichia coli ATCC 11775 and another typed fungal strain of Candida albicans (ATCC 90028) were also included. The study also intended to verify if the concomitant administration of conventional antibiotics with Ocimium gratisimum which is normally taken as food (spice) will negatively affect its activity.
Scalable inference in latent variable models

Latent variable techniques are pivotal in tasks ranging from predicting user click patterns and targeting ads to organizing the news and managing user generated content. Latent variable techniques like topic modeling, clustering, and subspace estimation provide substantial insight into the latent structure of complex data with little or no external guidance making them ideal for reasoning about large-scale, rapidly evolving datasets. Unfortunately, due to the data dependencies and global state introduced by latent variables and the iterative nature of latent variable inference, latent-variable techniques are often prohibitively expensive to apply to large-scale, streaming datasets. In this paper we present a scalable parallel framework for efficient inference in latent variable models over streaming web-scale data. Our framework addresses three key challenges: 1) synchronizing the global state which includes global latent variables (e.g., cluster centers and dictionaries); 2) efficiently storing and retrieving the large local state which includes the data-points and their corresponding latent variables (e.g., cluster membership); and 3) sequentially incorporating streaming data (e.g., the news). We address these challenges by introducing: 1) a novel delta-based aggregation system with a bandwidth-efficient communication protocol; 2) schedule-aware out-of-core storage; and 3) approximate forward sampling to rapidly incorporate new data. We demonstrate state-of-the-art performance of our framework by easily tackling datasets two orders of magnitude larger than those addressed by the current state-of-the-art. Furthermore, we provide an optimized and easily customizable open-source implementation of the framework1.
Underwater Image Enhancement by Dehazing With Minimum Information Loss and Histogram Distribution Prior

Images captured under water are usually degraded due to the effects of absorption and scattering. Degraded underwater images show some limitations when they are used for display and analysis. For example, underwater images with low contrast and color cast decrease the accuracy rate of underwater object detection and marine biology recognition. To overcome those limitations, a systematic underwater image enhancement method, which includes an underwater image dehazing algorithm and a contrast enhancement algorithm, is proposed. Built on a minimum information loss principle, an effective underwater image dehazing algorithm is proposed to restore the visibility, color, and natural appearance of underwater images. A simple yet effective contrast enhancement algorithm is proposed based on a kind of histogram distribution prior, which increases the contrast and brightness of underwater images. The proposed method can yield two versions of enhanced output. One version with relatively genuine color and natural appearance is suitable for display. The other version with high contrast and brightness can be used for extracting more valuable information and unveiling more details. Simulation experiment, qualitative and quantitative comparisons, as well as color accuracy and application tests are conducted to evaluate the performance of the proposed method. Extensive experiments demonstrate that the proposed method achieves better visual quality, more valuable information, and more accurate color restoration than several state-of-the-art methods, even for underwater images taken under several challenging scenes.
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Ultrastructural studies of human lymphoid cells. mu and J chain expression as a function of B cell differentiation

J chain expression was examined as a function of the stage in differentiation along the B cell axis in humans. Intracellular distribution of J and mu chains in leukemic HLA-DR+ null and pre-B cells, and in normal B cells stimulated with pokeweed mitogen (PWM) was determined by immunoelectron microscopy and radioimmunoassay (RIA). J chain was detected in leukemic null and pre-B cells on free and membrane-bound ribosomes in the cytoplasm, or on perinuclear cisternae. Mu chain was found on free ribosomes and ribosomal clusters in leukemic pre-B cells but was absent in the leukemic null cells. In pre-B cell lines, mu chain was seen within rough endoplasmic reticulum (RER) and the Golgi apparatus whereas J chain was not detected in these organelles. However, both mu and J chain were detected in RER and the Golgi apparatus of immature and mature plasma cells induced by PWM stimulation of normal peripheral blood lymphocytes. Low levels of J chain were also detected by RIA in lysates of leukemic null and pre-B cells. Most of the intracellular J chain became detectable after reduction and alkylation of cell lysates, and free J chain was not found in the culture supernatants. The amount of intracellular and secreted immunoglobulin-bound J chain increased dramatically after PWM stimulation of peripheral blood lymphocytes. The majority of J chain- positive cells seen over an 8 d culture interval were lymphocytes and lymphoblasts, while mu chain was found primarily in plasma cells. These results suggest that J chain expression precedes mu chain synthesis during B cell differentiation and that a combination of the two chains for secretion is not initiated until the onset of plasma cells maturation.
Zafirlukast Inhibits Complexation of Lsr2 with DNA and Growth of Mycobacterium tuberculosis

ABSTRACT The mycobacterial nucleoid-associated protein Lsr2 is a DNA-bridging protein that plays a role in condensation and structural organization of the genome and acts as a global repressor of gene transcription. Here we describe experiments demonstrating that zafirlukast inhibits the complexation between Lsr2 and DNA in vitro. Zafirlukast is shown to inhibit growth in two different species of mycobacteria tested but exhibits no growth inhibition of Escherichia coli. The Lsr2 inhibitory activity is reflected in vivo as determined by monitoring of transcription levels in Mycobacterium tuberculosis. These data suggest that zafirlukast inhibits Lsr2 function in vivo, promoting dysregulation of the expression of an array of genes typically bound by Lsr2 and hindering growth. Since zafirlukast likely operates by a mechanism distinct from current M. tuberculosis drugs and is currently used as a prophylactic treatment for asthma, it offers an intriguing lead for development of new treatments for tuberculosis.
Interactions between COX-2 and the renin-angiotensin system in the kidney.

AIM In adult mammalian kidney, COX-2 expression is found in a restricted subpopulation of cells. The two sites of renal COX-2 localization detected in all species to date are the macula densa (MD) and associated cortical thick ascending limb cells (cTALH) and medullary interstitial cells. Physiological regulation of COX-2 in these cellular compartments suggests functional roles for eicosanoid products of the enzyme. In the MD region, COX-2 expression increases in high renin states [salt restriction, angiotensin converting enzyme (ACE) inhibition, renovascular hypertension], and selective COX-2 inhibitors significantly decrease plasma renin levels and renal renin activity and mRNA expression. An important role for COX-2-derived prostanoids in regulation of renin expression and secretion has also been determined by using mice with selective genetic deletion of either the COX-1 or COX-2 gene. There is evidence for negative regulation of MD/cTALH COX-2 by angiotensin II and by glucocorticoids and mineralocorticoids, suggesting that in the kidney, cortical COX-2 expression is regulated in part by alterations in activity of the renin-angiotensin system.
Cellular heterogeneity profiling by hyaluronan probes reveals an invasive but slow-growing breast tumor subset

Significance Tumor heterogeneity is a poorly understood phenomenon. We lack biomarkers for identifying aggressive primary tumor subsets that give rise to metastases and impact early cancer detection and treatment. Many solid tumors are known to accumulate hyaluronan (HA), a glycosaminoglycan, which is also produced by the tumor cells themselves. We report a quantitative approach for uncovering breast cancer heterogeneity using fluorescent HA to detect differential binding patterns to CD44 and RHAMM/HMMR receptors. This approach permits identification of tumor-cell subsets that bind high levels of HA, and may be applicable to other ligands/receptors and disease models. Despite representing the invasive/metastatic subset of parental tumors, unexpectedly, the high HA-binding subset was slow-growing, and is thus likely to be a source of dormancy and relapse. Tumor heterogeneity confounds cancer diagnosis and the outcome of therapy, necessitating analysis of tumor cell subsets within the tumor mass. Elevated expression of hyaluronan (HA) and HA receptors, receptor for HA-mediated motility (RHAMM)/HA-mediated motility receptor and cluster designation 44 (CD44), in breast tumors correlates with poor outcome. We hypothesized that a probe for detecting HA–HA receptor interactions may reveal breast cancer (BCa) cell heterogeneity relevant to tumor progression. A fluorescent HA (F-HA) probe containing a mixture of polymer sizes typical of tumor microenvironments (10–480 kDa), multiplexed profiling, and flow cytometry were used to monitor HA binding to BCa cell lines of different molecular subtypes. Formulae were developed to quantify binding heterogeneity and to measure invasion in vivo. Two subsets exhibiting differential binding (HA−/low vs. HAhigh) were isolated and characterized for morphology, growth, and invasion in culture and as xenografts in vivo. F-HA–binding amounts and degree of heterogeneity varied with BCa subtype, were highest in the malignant basal-like cell lines, and decreased upon reversion to a nonmalignant phenotype. Binding amounts correlated with CD44 and RHAMM displayed but binding heterogeneity appeared to arise from a differential ability of HA receptor-positive subpopulations to interact with F-HA. HAhigh subpopulations exhibited significantly higher local invasion and lung micrometastases but, unexpectedly, lower proliferation than either unsorted parental cells or the HA−/low subpopulation. Querying F-HA binding to aggressive tumor cells reveals a previously undetected form of heterogeneity that predicts invasive/metastatic behavior and that may aid both early identification of cancer patients susceptible to metastasis, and detection/therapy of invasive BCa subpopulations.
Reuse within a cell-interference rejection or multiuser detection?

We investigate the use of an antenna array at the receiver in FDMA/TDMA systems, to let several users share one communication channel within a cell. A decision feedback equalizer which simultaneously detects all incoming signals (multiuser detection) is compared to a set of decision feedback equalizers, each detecting one signal and rejecting the remaining as interference. We also introduce the existence of a zero-forcing solution to the equalization problem as an indicator of near-far resistance of different detector structures. Simulations indicate that multiuser detection in general provides better performance than interference rejection. We have applied the proposed algorithms to experimental measurements from a DCS-1800 antenna array testbed. The results from these experiments confirm that reuse within a cell is indeed possible using an eight-element array antenna at the receiver.