Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV-1 transmission, by stage of infection.

BACKGROUND The epidemiological impact of public health interventions targeted at reducing transmission of human immunodeficiency virus type 1 (HIV-1) during early or late-stage infection depends on the contribution of these disease stages to transmission within a particular epidemic. METHODS Transmission hazards and durations of periods of high infectivity during primary, asymptomatic, and late-stage infection were estimated for HIV-1-serodiscordant heterosexual couples in Rakai, Uganda, by use of a robust probabilistic framework. RESULTS Primary infection and late-stage infection were estimated to be 26 and 7 times, respectively, more infectious than asymptomatic infection. High infectiousness during primary infection was estimated to last for approximately 3 months after seroconversion, whereas high infectiousness during late-stage infection was estimated to be concentrated between 19 months and 10 months before death. CONCLUSIONS Primary and late-stage HIV-1 infection are more infectious than previously estimated, but for shorter periods. In a homogeneous population, the asymptomatic stage of infection will typically contribute more to the net transmission of HIV-1 over the lifetime of an infected individual, because of its longer duration. The dependence of the relative contribution of infectious stages on patterns of sexual behavior and the phase of epidemics is discussed.
THE LYMPHOCYTE RESPONSE TO PRIMARY MOLONEY SARCOMA VIRUS TUMORS IN BALB/c MICE

Adult BALB/c mice were injected with Moloney sarcoma virus (MSV) after which the animals' lymphocytes were examined for activity against Moloney leukemia virus (MLV) antigen-bearing target cells at 5-day intervals for 30 days. Lymphocytes from these animals and appropriately matched controls were fractionated into B cell-deficient (primarily T cells) and T cell-deficient (primarily B cells) subpopulations. Macrophages were removed using iron powder and magnetism. The unfractionated lymphocytes, T cells, and non-T cells were then tested in microcytotoxicity tests. Antigen-specific activity was found in the unfractionated lymphocytes from animals that had not yet developed palpable tumors and from regressor animals. The T cells were active just before tumor development and just after regression; however, by day 30 after virus infection (8–10 days after regression) the T cell subpopulation was much less active. The non-T cell subpopulation was also active before tumor development and soon after regression. However, this activity continued to rise after regression and was highest at 30 days. At day 15 (peak tumor size) neither subpopulation was active. The activity was demonstrated to be specific for the MLV-determined cell surface antigen by testing on control target cells that were MLV antigen negative and by comparison of the inhibitory effects with lymphocytes immune to a nonpertinent antigen as well as normal lymphocytes. The non-T cells were tested for activity before and after removal of macrophages with iron powder and magnetism. Such cells were significantly more active after removal of the macrophages. These data demonstrate specific T cell and non-T cell activity in microcytotoxicity tests with a tumor-specific system and strongly suggest that the non-T cell activity described herein is a B cell function.
Establishing a cord blood banking and transplantation program in Mexico: a single institution experience

BACKGROUND: Over the past decade, umbilical cord blood (UCB) banking and transplantation have increased significantly worldwide. The experience in developing countries, however, is still limited. In January 2005 the Mexican Institute of Social Security (IMSS) initiated its UCB banking and transplantation program. This study reports on the experience generated at this institution during the first 2 years of activities.
A Singular Value Thresholding Algorithm for Matrix Completion

This paper introduces a novel algorithm to approximate the matrix with minimum nuclear norm among all matrices obeying a set of convex constraints. This problem may be understood as the convex relaxation of a rank minimization problem and arises in many important applications as in the task of recovering a large matrix from a small subset of its entries (the famous Netflix problem). Off-the-shelf algorithms such as interior point methods are not directly amenable to large problems of this kind with over a million unknown entries. This paper develops a simple first-order and easy-to-implement algorithm that is extremely efficient at addressing problems in which the optimal solution has low rank. The algorithm is iterative, produces a sequence of matrices $\{\boldsymbol{X}^k,\boldsymbol{Y}^k\}$, and at each step mainly performs a soft-thresholding operation on the singular values of the matrix $\boldsymbol{Y}^k$. There are two remarkable features making this attractive for low-rank matrix completion problems. The first is that the soft-thresholding operation is applied to a sparse matrix; the second is that the rank of the iterates $\{\boldsymbol{X}^k\}$ is empirically nondecreasing. Both these facts allow the algorithm to make use of very minimal storage space and keep the computational cost of each iteration low. On the theoretical side, we provide a convergence analysis showing that the sequence of iterates converges. On the practical side, we provide numerical examples in which $1,000\times1,000$ matrices are recovered in less than a minute on a modest desktop computer. We also demonstrate that our approach is amenable to very large scale problems by recovering matrices of rank about 10 with nearly a billion unknowns from just about 0.4% of their sampled entries. Our methods are connected with the recent literature on linearized Bregman iterations for $\ell_1$ minimization, and we develop a framework in which one can understand these algorithms in terms of well-known Lagrange multiplier algorithms.
Effector CD8 T Cell Development: A Balancing Act between Memory Cell Potential and Terminal Differentiation1

Immune responses to infection are optimally designed to generate large numbers of effector T cells while simultaneously minimizing the collateral damage of their potentially lethal actions and generating memory T cells to protect against subsequent encounter with pathogens. Much remains to be discovered about how these equally essential processes are balanced to enhance health and longevity and, more specifically, what factors control effector T cell expansion, differentiation, and memory cell formation. The innate immune system plays a prominent role in the delicate balance of these decisions. Insights into these questions from recent work in the area of effector CD8 T cell differentiation will be discussed.
Vasoactive intestinal peptide and pituitary adenylate cyclase‐activating polypeptide inhibit the production of inflammatory mediators by activated microglia

Microglia play a central role in the regulation of immune and inflammatory activities, as well as tissue remodeling in the central nervous system. However, activation of microglia is a histopathological hallmark of several neurodegenerative diseases. Pathological microglial activation is believed to contribute to progressive damage in neurodegenerative diseases through the release of proinflammatory and/or cytotoxic factors, including tumor necrosis factor α (TNF‐α), interleukin (IL)‐1β, IL‐6, IL‐12, and nitric oxide (NO). Hence, it is important to unravel mechanisms regulating microglia activation of inflamed brain parenchyma to provide insights into efficient therapeutic intervention. This study examines the role of two anti‐inflammatory neuropeptides, the vasoactive intestinal peptide (VIP) and the pituitary adenylate cyclase‐activating polypeptide (PACAP) on the production of various proinflammatory factors by endotoxin‐stimulated miroglia. VIP and PACAP inhibit TNF‐α, IL‐1β, IL‐6, and NO production by lipopolysaccharide (LPS)‐activated microglia. The specific type 1 VIP receptor mediates the inhibitory effect of VIP/PACAP, and cyclic adenosine monophosphate is the major, second messenger involved. VIP and PACAP regulate the production of these proinflammatory factors at a transcriptional level by inhibiting p65 nuclear translocation and nuclear factor‐κB‐DNA binding. This effect is mediated, as neuropeptides stabilize the inhibitor IκB by inhibiting LPS‐induced IκB‐kinase activity. Therefore, the inhibitory effects on the production of proinflammatory mediators define VIP and PACAP as “microglia‐deactivating factors” with significant, therapeutical potential for inflammatory/degenerative brain disorders.
Genetic Variants in Epidermal Growth Factor Receptor Pathway Genes and Risk of Esophageal Squamous Cell Carcinoma and Gastric Cancer in a Chinese Population

The epidermal growth factor receptor (EGFR) signaling pathway regulates cell proliferation, differentiation, and survival, and is frequently dysregulated in esophageal and gastric cancers. Few studies have comprehensively examined the association between germline genetic variants in the EGFR pathway and risk of esophageal and gastric cancers. Based on a genome-wide association study in a Han Chinese population, we examined 3443 SNPs in 127 genes in the EGFR pathway for 1942 esophageal squamous cell carcinomas (ESCCs), 1758 gastric cancers (GCs), and 2111 controls. SNP-level analyses were conducted using logistic regression models. We applied the resampling-based adaptive rank truncated product approach to determine the gene- and pathway-level associations. The EGFR pathway was significantly associated with GC risk (P = 2.16×10−3). Gene-level analyses found 10 genes to be associated with GC, including FYN, MAPK8, MAP2K4, GNAI3, MAP2K1, TLN1, PRLR, PLCG2, RPS6KB2, and PIK3R3 (P<0.05). For ESCC, we did not observe a significant pathway-level association (P = 0.72), but gene-level analyses suggested associations between GNAI3, CHRNE, PAK4, WASL, and ITCH, and ESCC (P<0.05). Our data suggest an association between specific genes in the EGFR signaling pathway and risk of GC and ESCC. Further studies are warranted to validate these associations and to investigate underlying mechanisms.
Finely Orchestrated Movements: Evolution of the Ribosomal RNA Genes

Evolution of the tandemly repeated ribosomal RNA (rRNA) genes is intriguing because in each species all units within the array are highly uniform in sequence but that sequence differs between species. In this review we summarize the origins of the current models to explain this process of concerted evolution, emphasizing early studies of recombination in yeast and more recent studies in Drosophila and mammalian systems. These studies suggest that unequal crossover is the major driving force in the evolution of the rRNA genes with sister chromatid exchange occurring more often than exchange between homologs. Gene conversion is also believed to play a role; however, direct evidence for its involvement has not been obtained. Remarkably, concerted evolution is so well orchestrated that even transposable elements that insert into a large fraction of the rRNA genes appear to have little effect on the process. Finally, we summarize data that suggest that recombination in the rDNA locus of higher eukaryotes is sufficiently frequent to monitor changes within a few generations.
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Pressure‐Flow Studies in Man During the Valsalva Maneuver with Observations on the Mechanical Properties of the Ascending Aorta

The pressure-gradient technique was used to obtain continuous measurements of both blood pressure and flow in the ascending aorta of eight normal subjects who were performing a standardized Valsalva maneuver. From these recordings the beat-to-beat changes in stroke volume, peak blood flow, peripheral vascular resistance, duration of ejection, and an index of total systolic duration were calculated. Stroke volume and peak blood flow were not changed with the onset of straining (phase I), but were decreased to approximately 50% of control values immediately prior to release (phase II). During the overshoot period (phase IV) stroke volume and peak flow were increased above control levels. Both the duration of ejection and the duration of systole were shortened during straining (phase II). The concomitant changes in blood pressure in these subjects were similar to previously reported pressure recordings. An estimate of the pressure-radius relationships in the ascending aorta of these patients was obtained angiographically. The mean cross-sectional area of the ascending aorta changed by 17% during the Valsalva maneuver.
MotionCast: on the capacity and delay tradeoffs

In this paper, we define multicast for ad hoc network through nodes' mobility as <i>MotionCast</i>, and study the capacity and delay tradeoffs for it. Assuming nodes move according to an independently and identically distributed (i.i.d.) pattern and each desires to send packets to <i>k</i> distinctive destinations, we compare the capacity and delay in two transmission protocols: one uses 2-hop relay algorithm without redundancy, the other adopts the scheme of redundant packets transmissions to improve delay while at the expense of the capacity. In addition, we obtain the maximum capacity and the minimum delay under certain constraints. We find that the per-node capacity and delay for 2-hop algorithm <i>without redundancy</i> are Θ(1/<i>k</i>) and Θ(<i>n</i>log <i>k</i>), respectively; and for 2-hop algorithm <i>with redundancy</i> they are Ω(1/(<i>k</i>√<i>n</i>log <i>k</i>)) and Θ(√<i>n</i>log <i>k</i>), respectively. The capacity of the 2-hop relay algorithm without redundancy is better than the multicast capacity of static networks developed in [3] as long as <i>k</i> is strictly less than <i>n</i> in an order sense; while when <i>k</i>=Θ(<i>n</i>), mobility does not increase capacity anymore. The ratio between delay and capacity satisfies <i>delay/rate</i> ≥ <i>O</i>(<i>nk</i>log <i>k</i>) for these two protocols, which is smaller than that of directly extending the fundamental tradeoff for unicast established in [1] to multicast, i.e., <i>O</i>(<i>nk</i><sup>2</sup>).
Sensitivity and specificity of median nerve ultrasonography in diagnosis of carpal tunnel syndrome

Background Although controversial, recent studies have demonstrated advantages of sonographic techniques in the diagnosis of carpal tunnel syndrome (CTS). The purpose of this study was to assess the utility of median nerve ultrasonography in the diagnosis of CTS in Iranian patients. Methods Ninety patents with clinically suspected CTS were studied. Based on gold standard electromyography/nerve conduction velocity studies, wrists with CTS were divided into three groups on the basis of severity of CTS, ie, mild, moderate, and severe. In addition, both sides of the wrist were examined using sonography. Transverse images of the median nerve were obtained and median nerve cross-section areas were measured at three levels, ie, immediately proximal to the carpal tunnel inlet, at the carpal tunnel inlet, and at the carpal tunnel outlet. Furthermore, flexor retinaculum thickness was evaluated. Results The mean age of the studied patients was 48.52 ± 12.17 years. Median values of the median nerve cross-section at the carpal tunnel inlet, carpal tunnel outlet, and proximal carpal tunnel significantly differed between the wrists with and without CTS (P < 0.05). Comparisons between the CTS groups (mild, moderate, and severe) and non-CTS wrists demonstrated that the median cross-sections of median nerve at the carpal tunnel inlet, carpal tunnel outlet, and inlet proximal carpal tunnel were significantly greater in the severe CTS group than in the other three groups (P < 0.05). The results showed that the median nerve cross-section at the three levels of carpal tunnel could only fairly differentiate severe CTS from other cases. Conclusion The present study demonstrated that median nerve ultrasonography cannot replace the gold standard test (nerve conduction velocity) for the diagnosis of CTS because of low overall sensitivity and specificity, although it might provide useful information in some patients.
Perfect genetic correlation between number of offspring and grandoffspring in an industrialized human population

Significance Reproductive success (offspring quantity) is widely used as a measure of fitness (genetic contribution to future generations). Accurate predictions of the direction and magnitude of evolutionary change using this measure depend on the untested assumption that the genes influencing number of offspring are the same as those influencing number of grandoffspring. Using a population sample of identical and nonidentical Swedish twins and their descendants, we show that the genetic influences on number of offspring and grandoffspring are identical, supporting the use of reproductive success as a measure of fitness in comparable human populations. Reproductive success is widely used as a measure of fitness. However, offspring quantity may not reflect the genetic contribution to subsequent generations if there is nonrandom variation in offspring quality. Offspring quality is likely to be an important component of human fitness, and tradeoffs between offspring quantity and quality have been reported. As such, studies using offspring quantity as a proxy for fitness may yield erroneous projections of evolutionary change, for example if there is little or no genetic variance in number of grandoffspring or if its genetic variance is to some extent independent of the genetic variance in number of offspring. To address this, we performed a quantitative genetic analysis on the reproductive history of 16,268 Swedish twins born between 1915 and 1929 and their offspring. There was significant sex limitation in the sources of familial variation, but the magnitudes of the genetic and environmental effects were the same in males and females. We found significant genetic variation in number of offspring and grandoffspring (heritability = 24% and 16%, respectively), and genetic variation in the two variables completely overlapped—i.e., there was a perfect genetic correlation between number of offspring and grandoffspring. Shared environment played a smaller but significant role in number of offspring and grandoffspring; again, there was a perfect shared environmental correlation between the two variables. These findings support the use of lifetime reproductive success as a proxy for fitness in populations like the one used here, but we caution against generalizing this conclusion to other kinds of human societies.
Automatic Threshold Selection using PSO for GA based Duplicate Record Detection

Normally setting the threshold is an important issue in applications where the similarity functions are used and it relies more on human intervention. The proposed work addressed two issues : first to find the optimal equation using Genetic Algorithm (GA) and next it adopts an intelligence algorithm, Particle Swarm Optimization (PSO) to get the optimal threshold to detect the duplicate records more accurately and also it reduces human intervention. Restaurant and CORA data repository are used to analyze the proposed algorithm and the performance of the proposed algorithm is compared against marlin method and the genetic programming with the help of evaluation metrics.
Sources of high temperature degradation of cement-based materials : nanoindentation and microporoelastic analysis

The effects of high temperature exposure on cement-based materials have been under investigation for quite some time, but a fundamental understanding of the sources of high temperature degradation has been limited by measurement capabilities. Using recent developments in nanotechnology and microporoelastic modeling, this study identifies sources of high temperature degradation at the nanoscale for the first time. For reference and comparison with existing literature, the traditional methods of thermogravimetry, uniaxial compression, and resonant frequency are used to measure mass loss, compressive strength and elastic modulus, respectively. However, microscopic measurement of the elastic modulus and hardness is the primary experimental focus of this study. Microindentation is used to measure the properties of homogenized cement paste, whereas nanoindentation is used to measure the properties of the various phases which make up cement paste. All experimental methods are performed on cement paste subjected to specified investigation temperatures ranging from 25 0C to 700'C. Using experimental results in combination with data in the literature, microporoelastic modeling is used to identify the sources of high temperature elasticity degradation which are inherent to each cement paste phase. Only through this unique combination of experimental and theoretical investigations are two primary sources of high temperature elasticity degradation separately identified at the nanoscale: 1) dehydration (loss of bound water) within the elementary building block of C-S-H, and 2) a decrease in packing density of both the low-density and high-density C-S-H phases above 300 0C. Based on these identified sources of high temperature elasticity degradation, a model which predicts the elasticity of cement paste as a function of temperature (up to 700'C) is developed. Thesis Supervisor: Franz-Josef Ulm Title: Associate Professor of Civil and Environmental Engineering
On brane–antibrane forces

In this note, we will discuss two aspects of brane–antibrane forces. In one aspect, we generalize the force calculation of D0-0 of Banks and Susskind to Dp-p for 1 ≤ p ≤ 8. In particular, we find that the force is also divergent for p = 1 while for the other cases (p ≥ 2) the forces are in general finite when Z → 0+, where Z = (Y2)/(2π2α')−1 with Y, the brane–antibrane separation. However, the forces are divergent for all cases when Z < 0, signalling the occurrence of open string tachyon condensation in this regime. The other deals with the puzzling static nature of the supergravity brane–antibrane configurations. We will show that the force on a brane probe due to a brane–antibrane background vanishes when the probe is placed at the location of the coincident brane–antibranes, thereby providing a direct evidence for the existence of general static brane–antibrane configuration in the supergravity approximation.