Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell death under epithelial–mesenchymal transition control in prostate cancer therapeutic response

Prostate cancer is a widespread problem among men, with >160 000 new cases in 2017 alone. Androgen deprivation therapy is commonly used in prostate cancer treatment to block androgens required for cancer growth, but disease relapse after androgen deprivation therapy is both common and severe. Changes in androgen receptor signaling from androgen deprivation therapy have been linked to therapeutic resistance and tumor progression. Resistant cells can become reprogrammed to undergo epithelial–mesenchymal transition, a phenotypic switch from benign, epithelial cells to a mobile cell with mesenchymal traits. In these cells, attachment to their epithelial cell layer is no longer required for survival. Anoikis is a form of cell death that occurs when detachment from other cells and the basement membrane occurs. Epithelial cells have been shown to undergo epithelial–mesenchymal transition, avoid anoikis induction and progress to a metastatic phenotype. In prostate cancer progression to advanced disease, epithelial–mesenchymal transition induction (characterized by loss of epithelial cellular attachment protein E‐cadherin) correlates with a higher Gleason score, tumor progression, increased metastasis and higher biochemical recurrence. The concept of interfacing epithelial–mesenchymal transition with anoikis in the tumor microenvironment landscape will be discussed here, with focus on the significance of the functional exchange between the two processes in therapeutic targeting of advanced disease. The current evidence on the impact of loss of cell–cell contact, acquisition of chemoresistance, immune escape and metastatic spread in advanced tumors in response to transforming growth factor‐β on prostate cancer metastasis will be also discussed. The signaling cross‐talk between transforming growth factor‐β and androgen receptor signaling will be interrogated as a new therapeutic platform for the development of combination strategies to impair prostate cancer metastasis.
Risk Factors That Increase Risk of Estrogen Receptor–Positive and –Negative Breast Cancer

Background Risk factors may differentially influence development of estrogen receptor (ER)-positive vs -negative breast cancer. We examined associations with strong, prevalent risk factors by ER subtype. Methods Of 1 279 443 women age 35 to 74 years participating in the Breast Cancer Surveillance Consortium, 14 969 developed ER-positive and 3617 developed ER-negative invasive breast cancer. We calculated hazard ratios (HRs) using Cox regression and compared ER subtype hazard ratios at representative ages or by menopausal status using Wald tests. All statistical tests were two-sided. Results For women age 40 years, compared with no prior biopsy, ER-positive vs ER-negative HRs were 1.53 (95% CI = 1.30 to 1.81) vs 1.26 (95% CI = 0.90 to 1.76) for nonproliferative disease, 1.63 (95% CI = 1.23 to 2.17) vs 1.41 (95% CI = 0.78 to 2.57) for proliferative disease without atypia, and 4.47 (95% CI = 2.88 to 6.96) vs 0.20 (95% CI = 0.02 to 2.51) for proliferative disease with atypia. Benign disease proliferation risk was stronger for ER-positive than ER-negative cancer for women age 35 years (Wald P = .04), age 40 years (Wald P = .04), and age 50 years (Wald P = .06). Among pre/perimenopausal women, body mass index (BMI) had a stronger association with ER-negative than ER-positive cancer (obese II/III vs. normal weight: HR = 1.52, 95% CI = 1.19 to 1.94; vs 1.21, 95% CI = 1.08 to 1.36). Increasing BMI similarly increased ER-positive and ER-negative cancer risk among postmenopausal hormone users (Wald P = .15) and nonusers (Wald P = .08). Associations with ER subtype varied by race/ethnicity across all ages (P < .001) and by family history of breast cancer and breast density for specific ages. Conclusions Strength of risk factor associations differed by ER subtype. Separate risk models for ER subtypes may improve identification of women for targeted prevention strategies.
Mixed-stock analysis in green turtles Chelonia mydas: mtDNA decipher current connections among west Atlantic populations

Abstract The green turtle Chelonia mydas undertakes wide-ranging migrations between feeding and nesting sites, resulting in mixing and isolation of genetic stocks. We used mtDNA control region to characterize the genetic composition, population structure, and natal origins of C. mydas in the West Atlantic Ocean, at one feeding ground (State of Rio de Janeiro, Brazil), and three Caribbean nesting grounds (French Guiana, Guadeloupe, and Suriname). The feeding ground presented considerable frequency of common haplotypes from the South Atlantic, whereas the nesting sites presented a major contribution of the most common haplotype from the Caribbean. MSA revealed multiple origins of individuals at the feeding ground, notably from Ascension Island, Guinea Bissau, and French Guiana. This study enables a better understanding of the dispersion patterns and highlights the importance of connecting both nesting and feeding areas. Effective conservation initiatives need to encompass these ecologically and geographically distinct sites as well as those corridors connecting them.
Performance of HbA1c as an Early Diagnostic Indicator of Type 1 Diabetes in Children and Youth

OBJECTIVE The aim of this study was to evaluate HbA1c as an alternative criterion for impaired glucose tolerance (IGT) or type 1 diabetes (T1D) in high-risk subjects <21 years of age. RESEARCH DESIGN AND METHODS Subjects <21 years of age who participated in the prospective DPT-1, TEDDY, TRIGR, and Type 1 Diabetes TrialNet Natural History (TrialNet) studies and had an HbA1c within 90 days of an OGTT with a 2-h plasma glucose (2-hPG) measure were included. An OGTT of 140–199 mg/dL defined IGT, and an OGTT with 2-hPG ≥200 mg/dL or fasting plasma glucose ≥126 mg/dL defined diabetes. HbA1c ≥5.7% defined IGT, and HbA1c ≥ 6.5% defined diabetes. Receiver-operating characteristic curve analysis was used to assess diagnostic accuracy of HbA1c compared with OGTT. RESULTS There were 587 subjects from DPT-1, 884 from TrialNet, 91 from TEDDY, and 420 from TRIGR. As an indicator for IGT, HbA1c sensitivity was very low across the studies (8–42%), and specificity was variable (64–95%). With HbA1c ≥6.5% threshold used for T1D diagnosis, the sensitivity was very low and specificity was high (sensitivity and specificity: DPT-1 24 and 98%, TrialNet 28 and 99%, TEDDY 34 and 98%, and TRIGR 33 and 99%, respectively). The positive predictive value of HbA1c ≥6.5% for the development of T1D was variable (50–94%) across the four studies. CONCLUSIONS HbA1c ≥6.5% is a specific but not sensitive early indicator for T1D in high-risk subjects <21 years of age diagnosed by OGTT or asymptomatic hyperglycemia. Redefining the HbA1c threshold is recommended if used as an alternative criterion in diagnosing T1D.
Inadvertent Introduction of Tissue Coring Into Joints During Arthrocentesis: An Experimental Study

Background The aim of this study was to investigate whether needles introduce skin plugs into joints during arthrocentesis. Material/Methods In the first part of this study, the arthrocentesis site was scrubbed with a fluorescein sodium swab, and 90 needles were inserted through the joint tissue and collected for examination under a fluorescence microscope. In the second part of this study, the joints were injected using 720 needles of different gauges. Two different randomly assigned needle insertion techniques were used: needle insertion straight through the joint capsule (subgroup 1) or insertion of the needle into the subcutaneous tissue followed by flushing of the needle with 0.5 mL of 0.9% normal saline prior to advancing the needle through the joint capsule (subgroup 2). Results Of the 90 needle tips examined in the first part of this study, 21 had high-grade fluorescein contamination. In the second part of this study, the incidence of tissue, epidermis, and dermis contamination in subgroup 1 was 57.2%, 43.1%, and 25.0%, respectively. There was no significant difference in the incidence among different gauge needles, except for a difference in epidermis contamination between the 21-gauge and 23-gauge needles. Compared to subgroup 1, subgroup 2 had a significantly lower OR for tissue contamination. Conclusions It is common to introduce tissue coring with epidermis and dermis into the joint during arthrocentesis, which poses a potential risk for septic arthritis. However, tissue contamination of the joint may be reduced by flushing saline through the needle into the subcutaneous tissues prior to entering the joint capsule.
Processing diets containing corn distillers' dried grains with solubles in growing broiler chickens: effects on performance, pellet quality, ileal amino acids digestibility, and intestinal microbiota

ABSTRACT The present study investigated the effects of feed form and distillers' dried grains with solubles (DDGS) on growth performance, nutrient digestibility, and intestine microbiota in broilers. A total of 720 broilers (Ross 308; average BW 541 ± 6 g) was randomly allotted to 6 treatments on the basis of BW. There were 6 replicates in each treatment with 20 birds per replicate. Birds were fed 3 different feed forms (mash, simple pellet, and expanded pellet) and DDGS (0 or 20% of diet) in a 3 × 2 factorial arrangement. Simple pellet (SP) and expanded pellet (EP) fed birds showed an increase in BW gain (P < 0.05). The interaction between feed processing and DDGS level was observed on pellet hardness (P < 0.01). The lowest (P < 0.01) pellet durability index (PDI) and hardness were observed in the diet with DDGS. Values for PDI and hardness were higher for EP compared with SP (P < 0.01). Simple pellet decreased ileal digestibility of CP compared to mash feed. The inclusion of DDGS decreased the digestibility of CP, and tended to decrease digestibility of DM (P = 0.056) and gross energy (P = 0.069). Expanded pellet feeding decreased (P < 0.05) the ileal digestibility of isoleucine, lysine, methionine, phenylalanine, threonine, cysteine, and glutamine compared with mash diet. Processed feed increased (P < 0.01) pH in the gizzard and duodenum; however, processing decreased pH in ileum. The addition of DDGS to the diet reduced pH in the duodenum. The population of Lactobacillus spp. was lower in the duodenum of birds fed the EP diet compared to the mash diet. Processed feed increased the colonization of Clostridium spp. in the gizzard. These results indicated that SP and EP in broiler diet had a potential to improve BW gain, but EP compromised amino acid digestibility. In addition, DDGS supplementation (20%) decreased pellet quality and CP digestibility in broiler chickens; however, the growth performance and feed intake were not affected.
Consciousness as Inference in Time A Commentary on Victor Lamme

Unraveling the neural correlates of conscious remains one of the great challenges of our time. Victor Lamme proposes that neural integration through feedback loops is what differentiates conscious from unconscious processing. Here, I review his hypothesis, focusing on the spatial scale of integration as well as the possible neural mechanisms involved. I go on to show that any theory of the neural correlates of consciousness is incomplete if it cannot account for how prior knowledge shapes perception and how this form of integration occurs. Finally, I propose that integration across moments in time is a crucial but hitherto neglected aspect of conscious perception, which creates the “flow” of conscious experience.
A 1.9-mm-Precision 20-GHz Direct-Sampling Receiver Using Time-Extension Method for Indoor Localization

This paper presents an impulse-radio ultra-wideband (IR-UWB) receiver design for precise wireless ranging using a newly proposed direct sampling with time-extension (DTE) method. To overcome the problems encountered in high-speed sampling for impulse signals, the DTE method, which exploits the characteristics of an impulse, is proposed. The proposed method performs high-speed sampling only during the period when short pulses exist, and quantizes the sampled signal during the dead time where no pulses exist. The high-speed impulse signal can be easily digitized using low-speed analog-to-digital converter. We designed and fabricated the IR-UWB receiver using a 65-nm CMOS process. The measurement result shows a 1.9-mm resolution for indoor wireless ranging within a 1-m range. The receiver has a power consumption of 70 mW at 1.2 V and energy efficiency of 1554 nJ/pulse.
Design of Short Irregular LDPC Codes for a Markov-modulated Gaussian Channel

This paper deals with the design of short irregular Low-Density Parity-Check (LDPC) codes. An optimization method for the underlying symbol-node degree-distribution (SNDD) of an irregular LDPC code is introduced, which is based on the Downhill-Simplex (DHS) algorithm. In order to compare our method with the optimization described in (Hu et al., 2005), which is based on a simplified version of the DHS algorithm, we first designed a rate 0 . 5 irregular LDPC code of length n= 504 for an Additive White Gaussian Noise Channel (AWGNC). The proposed optimization method was then used to design an irregular LDPC code for a Markov-modulated Gaussian Channel (MMGC). The decoding performance of the resulting LDPC code is then compared to the design based on the Density-Evolution (DE) method.
Noncommutative Arithmetic Circuits meet Finite Automata

Ideas and tools from automata theory have often played a significant role in computational complexity. A prominent and well-known example is the fine structure of NC^1 which was discovered using automata theory and the classification of finite monoids [M. Ben-Or and P. Tiwari. A Deterministic Algorithm For Sparse Multivariate Polynomial Interpolation. STOC 1998] In this article we discuss some recent applications of basic automata theory to noncommutative arithmetic circuit complexity.
Duty-Cycle-Aware Minimum Latency Broadcast Scheduling in Multi-hop Wireless Networks

Broadcast is an essential and widely-used operation in multi-hop wireless networks. Minimum latency broadcast scheduling (MLBS) aims to provide a collision-free scheduling for broadcast with the minimum latency. Previous work on MLBS mostly assumes that nodes are always active, and thus is not suitable for duty-cycle-aware scenarios. In this paper, we investigate the duty-cycle-aware minimum latency broadcast scheduling (DCA-MLBS) problem in multi-hop wireless networks. We prove both the one-to-all and the all-to-all DCA-MLBS problems to be NP-hard. We propose a novel approximation algorithm called OTAB for the one-to-all DCA-MLBS problem, and two approximation algorithms called UTB and UNB for the all-to-all DCA-MLBS problem under the unit-size and the unbounded-size message models respectively. The OTAB algorithm achieves a constant approximation ratio of 17|T|, where |T| denotes the number of time-slots in a scheduling period. The UTB and UNB algorithms achieve the approximation ratios of 17|T|+20 and (Δ+22)|T| respectively, where Δ denotes the maximum node degree of the network. Extensive simulations are conducted to evaluate the performance of our algorithms.
Does Goal-Oriented Requirements Engineering Achieve Its Goal?

The number of papers and articles on goals would suggest that goal-oriented requirements engineering is a well understood and mature area within the requirements engineering discipline. In particular, there is a wealth of published material on formal goal modelling approaches. However, the uptake of the goal approaches advocated by academics and researchers within real world settings appears to be quite low. Where goals are used in industrial practice their use is mainly informal and the methods used are inconsistent. There appears to be a significant gap between research and practice in the use of goals within requirements engineering. A two-part study was undertaken to check whether there is evidence to support this view of a disconnection between research and industry. Firstly, a literature survey of requirements engineering papers about goals reveals a large body of published material, but the majority has little industrial involvement. Secondly, a questionnaire completed by experienced requirements engineering practitioners suggests that use of goals in practice is inconsistent, informal, and rarely utilises formal modelling approaches. This paper proposes future work that would close the gap between research and practice in the use of goals within requirements engineering.
Single-molecule Super-resolution Imaging of Phosphatidylinositol 4,5-bisphosphate in the Plasma Membrane with Novel Fluorescent Probes

Phosphoinositides in the cell membrane are signaling lipids with multiple cellular functions. Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is a determinant phosphoinositide of the plasma membrane (PM), and it is required to modulate ion channels, actin dynamics, exocytosis, endocytosis, intracellular signaling, and many other cellular processes. However, the spatial organization of PI(4,5)P2 in the PM is controversial, and its nanoscale distribution is poorly understood due to the technical limitations of research approaches. Here by utilizing single molecule localization microscopy and the Pleckstrin Homology (PH) domain based dual color fluorescent probes, we describe a novel method to visualize the nanoscale distribution of PI(4,5)P2 in the PM in fixed membrane sheets as well as live cells.
Development of Broadly Neutralizing Antibodies and Their Mapping by Monomeric gp120 in Human Immunodeficiency Virus Type 1-Infected Humans and Simian-Human Immunodeficiency Virus SHIVSF162P3N-Infected Macaques

ABSTRACT To improve our understanding of the similarities and differences between neutralizing antibodies elicited by simian-human immunodeficiency virus (SHIV)-infected rhesus macaques and human immunodeficiency virus type 1 (HIV-1)-infected humans, we examined the plasma of 13 viremic macaques infected with SHIVSF162P3N and 85 HIV-1-infected humans with known times of infection. We identified 5 macaques (38%) from 1 to 2 years postinfection (p.i.) with broadly neutralizing antibodies (bnAbs) against tier 2 HIV-1. In comparison, only 2 out of 42 (5%) human plasma samples collected in a similar time frame of 1 to 3 years p.i. exhibited comparable neutralizing breadths and potencies, with the number increasing to 7 out of 21 (30%) after 3 years p.i. Plasma mapping with monomeric gp120 identified only 2 out of 9 humans and 2 out of 4 macaques that contained gp120-reactive neutralizing antibodies, indicating distinct specificities in these plasma samples, with most of them recognizing the envelope trimer (including gp41) rather than the gp120 monomer. Indeed, a total of 20 gp120-directed monoclonal antibodies (MAbs) isolated from a human subject (AD358) and a Chinese rhesus macaque (GB40) displayed no or limited neutralizing activity against tier 2 strains. These isolated MAbs, mapped to the CD4-binding site, the V3 loop, the inner domain, and the C5 region of gp120, revealed genetic similarity between the human and macaque immunoglobulin genes used to encode some V3-directed MAbs. These results also support the use of envelope trimer probes for efficient isolation of HIV-1 bnAbs. IMPORTANCE HIV-1 vaccine research can benefit from understanding the development of broadly neutralizing antibodies (bnAbs) in rhesus macaques, commonly used to assess vaccine immunogenicity and efficacy. Here, we examined 85 HIV-1-infected humans and 13 SHIVSF162P3N-infected macaques for bnAbs and found that, similar to HIV-1-infected humans, bnAbs in SHIV-infected macaques are also rare, but their development might have been faster in some of the studied macaques. Plasma mapping with monomeric gp120 indicated that most bnAbs bind to the envelope trimer rather than the gp120 monomer. In support of this, none of the isolated gp120-reactive monoclonal antibodies (MAbs) displayed the neutralization breadth observed in the corresponding plasma. However, the MAb sequences revealed similarity between human and macaque genes used to encode some V3-directed MAbs. Our study sheds light on the timing and development of bnAbs in SHIV-infected macaques in comparison to HIV-1-infected humans and highlights the use of envelope trimer probes for efficient recovery of bnAbs.
Flexible and Scalable Deep Learning with MMLSpark

In this work we detail a novel open source library, called MMLSpark, that combines the flexible deep learning library Cognitive Toolkit, with the distributed computing framework Apache Spark. To achieve this, we have contributed Java Language bindings to the Cognitive Toolkit, and added several new components to the Spark ecosystem. In addition, we also integrate the popular image processing library OpenCV with Spark, and present a tool for the automated generation of PySpark wrappers from any SparkML estimator and use this tool to expose all work to the PySpark ecosystem. Finally, we provide a large library of tools for working and developing within the Spark ecosystem. We apply this work to the automated classification of Snow Leopards from camera trap images, and provide an end to end solution for the non-profit conservation organization, the Snow Leopard Trust.
An update-overhead-aware caching policy for write-optimized file systems on SMR disks

To accommodate the sheer volume of data in the era of Big Data and Cloud Computing, both new storage medium technologies and high-performance file systems are proposed. For storage medium, Shingled Magnetic Recording (SMR) increases the areal density by overlapping adjacent tracks so as to provide larger storage capacity. On the other hand, write-optimized indexes (WOI) file systems are also studied and can now outperform conventional file systems with orders of magnitude. However, the main drawback of SMR is the random-write restriction because random-write operations will cause the extra overhead of rewriting data stored in overlapped tracks. The rewriting overhead is amplified by the recursive entry update behavior of WOI-based file systems. Therefore, the rewriting issue becomes a serious performance overhead when adopting SMR drives as underlying storage devices for WOI-based file systems. To mitigate the write amplification problem when deploying WOI-based file systems on SMR disks, this paper proposes the update-overhead-aware caching policy to reduce the update overhead with the help of flash-based storage devices. To evaluate the performance of the proposed design, the B+-tree as a case study. The experimental results are promising.
Genetics of patella hypoplasia/agenesis

The patella is a sesamoid bone, crucial for knee stability. When absent or hypoplastic, recurrent knee subluxations, patellofemoral dysfunction and early gonarthrosis may occur. Patella hypoplasia/agenesis may be isolated or observed in syndromic conditions, either as the main clinical feature (Nail‐patella syndrome, small patella syndrome), as a clue feature which can help diagnosis assessment, or as a background feature that may be disregarded. Even in the latter, the identification of patella anomalies is important for an appropriate patient management. We review the clinical characteristics of these rare diseases, provide guidance to facilitate the diagnosis and discuss how the genes involved could affect patella development.