Miracle-dz/UniFAR-FTUs huggingface dataset:
Proximity biotinylation provides insight into the molecular composition of focal adhesions at the nanometer scale

Identification of proteins within nanometers of components in focal adhesions reveals potential targets for preventing metastasis. Focusing on focal adhesions Focal adhesions are protein complexes that link cells to the surrounding extracellular matrix, and their disassembly and reassembly are required during cell migration. The proteins in focal adhesions could be targeted to prevent cancer cell metastasis, but the composition of these complexes (which is generally referred to as the adhesome) has been controversial. Dong et al. used a label that targeted only proteins in close proximity to paxillin and β integrins, key components of focal adhesions. Mass spectrometry on the labeled proteins revealed that focal adhesions contained fewer proteins than previously suspected and identified several previously unknown components. After analysis of the function of these proteins in focal adhesions, they could be targeted to block metastasis. Focal adhesions are protein complexes that link metazoan cells to the extracellular matrix through the integrin family of transmembrane proteins. Integrins recruit many proteins to these complexes, referred to as the “adhesome. ” We used proximity-dependent biotinylation (BioID) in U2OS osteosarcoma cells to label proteins within 15 to 25 nm of paxillin, a cytoplasmic focal adhesion protein, and kindlin-2, which directly binds β integrins. Using mass spectrometry analysis of the biotinylated proteins, we identified 27 known adhesome proteins and 8 previously unknown components close to paxillin. However, only seven of these proteins interacted directly with paxillin, one of which was the adaptor protein Kank2. The proteins in proximity to β integrin included 15 of the adhesion proteins identified in the paxillin BioID data set. BioID also correctly established kindlin-2 as a cell-cell junction protein. By focusing on this smaller data set, new partners for kindlin-2 were found, namely, the endocytosis-promoting proteins liprin β1 and EFR3A, but, contrary to previous reports, not the filamin-binding protein migfilin. A model adhesome based on both data sets suggests that focal adhesions contain fewer components than previously suspected and that paxillin lies away from the plasma membrane. These data not only illustrate the power of using BioID and stable isotope–labeled mass spectrometry to define macromolecular complexes but also enable the correct identification of therapeutic targets within the adhesome.
Optimizing proton pump inhibitor therapy for treatment of nonvariceal upper gastrointestinal bleeding.

PURPOSE The pharmacology, rationale, and dosing optimization strategies of proton pump inhibitors (PPIs) for the treatment of upper gastrointestinal bleeding (UGIB) are discussed. SUMMARY In combination with endoscopic therapy, PPIs are the treatment of choice for UGIB. While the advent of PPIs has improved patient outcomes, controversy still exists over optimal PPI therapy for UGIB. Pharmacologic treatment in combination with endoscopic therapy has demonstrated improved outcomes in patients with nonvariceal UGIB. PPIs are the treatment of choice for suppressing gastric acid and preventing rebleeding, though a mortality benefit from these agents has not been strongly established. Although the current guidelines recommend an i.v. bolus injection followed by continuous infusion of a high-dose PPI, intermittent PPI therapy has been found to be safe and effective while significantly reducing cost, even in patients with high-risk stigmata after endoscopy. Oral PPIs may be effective in patients who can tolerate oral therapy but require further evaluation in patients with higher-risk stigmata. Regardless of stigmata, after 72 hours of i.v. therapy, patients with UGIB may be safely transitioned to oral PPIs if hemodynamically stable and able to tolerate oral medication. As the risk of rebleeding significantly decreases after the first three days, continuation of high-dose therapy beyond 72 hours is not necessary in hemodynamically stable patients. CONCLUSION Current guidelines recommend that PPIs be given as an i.v. bolus injection followed by a continuous infusion, but intermittent i.v. dosing and oral PPI therapy have been found to be effective in treating patients with UGIB and associated with reductions in cost.
Graph recursive least squares filter for topology inference in causal data processes

In this paper, we introduce the concept of recursive least squares graph filters for online topology inference in data networks that are modelled as Causal Graph Processes (CGP). A Causal Graph Process (CGP) is an auto regressive process in the time series associated to different variables, and whose coefficients are the so-called graph filters, which are matrix polynomials with different orders of the graph adjacency matrix. Given the time series of data at different variables, the goal is to estimate these graph filters, hence the associated underlying adjacency matrix. Previously proposed algorithms have focused on a batch approach, assuming implicitly stationarity of the CGP. We propose an online method for a recursive estimation of the adjacency matrix based on the sequential arrival of new data, which we call Graph Recursive Least Squares (GRLS) Filter. In addition to advantages in terms of complexity when compared to a batch approach, this method can also capture the dynamics of the underlying graph process and adapt to new observations. Our experimental results show that the GRLS algorithm has a low mean square error in terms of topology inference, and approaches the error associated to the batch solution rapidly as the number of data samples increases.
GSI: efficient spatio-temporal template for human gait recognition

Human gait recognition is a challenging task in computer vision community. In order to represent the gait, the most common feature is a gait template. Many efficient templates have been developed recently, however, the effectiveness of the proposed motion models is still under investigation. A novel template feature, named gait salient image (GSI) is introduced in this paper. The main contribution of the proposed GSI is encoding the motion energy of gait into a single template. This idea is being conceptualised by applying appropriate spatio-temporal filter for extracting motion features and averaging it over a gait period. To show how GSI-based feature is being efficient, the proposed template is classified using PCA+LDA. Extensive experiments on popular gait databases reveal an improvement over the available methods in terms of efficiency and accuracy. The value of recognition rate is 58.44% for Rank1 and 76.60% for Rank5 based on the USF database.
A Location Tracking System using BLE Beacon Exploiting a Double-Gaussian Filter

In this paper, we propose indoor location tracking method using RSSI(Received Signal Strength Indicator) value received from BLE(Bluetooth Low Energy) beacon. Due to the influence of various external environmental factors, it is very difficult to improve the accuracy in indoor location tracking. In order to solve this problem, we propose a novel method of reducing the noise generated in the external environment by using a double Gaussian filter. In addition, the value of the RSSI signal generated in the BLE beacon is different for each device. In this study, we propose a method to allocate additional weights in order to compensate the intensity of signal generated in each device. This makes it possible to improve the accuracy of indoor location tracking using beacons. The experiment results show that the proposed method effectively decrease the RSSI deviation and increase location accuracy. In order to verify the usefulness of this study, we compared the Kalman filter algorithm which is widely used in signal processing. We further performed additional experiments for application area for indoor location service and find that the proposed scheme is useful for BLE-based indoor location service.
Multimodal Mood Classification - A Case Study of Differences in Hindi and Western Songs

Music information retrieval has emerged as a mainstream research area in the past two decades. Experiments on music mood classification have been performed mainly on Western music based on audio, lyrics and a combination of both. Unfortunately, due to the scarcity of digitalized resources, Indian music fares poorly in music mood retrieval research. In this paper, we identified the mood taxonomy and prepared multimodal mood annotated datasets for Hindi and Western songs. We identified important audio and lyric features using correlation based feature selection technique. Finally, we developed mood classification systems using Support Vector Machines and Feed Forward Neural Networks based on the features collected from audio, lyrics, and a combination of both. The best performing multimodal systems achieved F-measures of 75.1 and 83.5 for classifying the moods of the Hindi and Western songs respectively using Feed Forward Neural Networks. A comparative analysis indicates that the selected features work well for mood classification of the Western songs and produces better results as compared to the mood classification systems for Hindi songs.
OFDM-Autoencoder for End-to-End Learning of Communications Systems

We extend the idea of end-to-end learning of communications systems through deep neural network (NN)-based autoencoders to orthogonal frequency division multiplexing (OFDM) with cyclic prefix (CP). Our implementation has the same benefits as a conventional OFDM system, namely single-tap equalization and robustness against sampling synchronization errors, which turned out to be one of the major challenges in previous single-carrier implementations. This enables reliable communication over multipath channels and makes the communication scheme suitable for commodity hardware with imprecise oscillators. We show that the proposed scheme can be realized with state-of-the-art deep learning software libraries as transmitter and receiver solely consist of differentiable layers required for gradient-based training. We compare the performance of the autoencoder-based system against that of a state-of-the-art OFDM baseline over frequency-selective fading channels. Finally, the impact of a non-linear amplifier is investigated and we show that the autoencoder inherently learns how to deal with such hardware impairments.
PRAS40 Connects Microenvironmental Stress Signaling to Exosome-Mediated Secretion

ABSTRACT Secreted exosomes carrying lipids, proteins, and nucleic acids conduct cell-cell communications within the microenvironment of both physiological and pathological conditions. Exosome secretion is triggered by extracellular or intracellular stress signals. Little is known, however, about the signal transduction between stress cues and exosome secretion. To identify the linker protein, we took advantage of a unique finding in human keratinocytes. In these cells, although transforming growth factor alpha (TGF-α) and epidermal growth factor (EGF) share the same EGF receptor and previously indistinguishable intracellular signaling networks, only TGF-α stimulation causes exosome-mediated secretion. However, deduction of EGF-activated pathways from TGFα-activated pathways in the same cells allowed us to identify the proline-rich Akt substrate of 40 kDa (PRAS40) as the unique downstream effector of TGF-α but not EGF signaling via threonine 308-phosphorylated Akt. PRAS40 knockdown (KD) or PRAS40 dominant-negative (DN) mutant overexpression blocks not only TGF-α- but also hypoxia- and H2O2-induced exosome secretion in a variety of normal and tumor cells. Site-directed mutagenesis and gene rescue studies show that Akt-mediated activation of PRAS40 via threonine 246 phosphorylation is both necessary and sufficient to cause exosome secretion without affecting the endoplasmic reticulum/Golgi pathway. Identification of PRAS40 as a linker protein paves the way for understanding how stress regulates exosome secretion under pathophysiological conditions.
Self-management in African American Women With Diabetes

Purpose This study describes demographic and medical characteristics, self-efficacy, locus of control, self-managementd defined by functional status, hemoglobin HbA1c outcomes, and the relationships among these variables based on age group differences (25-44 years, 45-64 years, and 65-84 years) in African American women with type 2 diabetes. Methods Subjects (n = 75) in community medical practices were interviewed to complete a demographic and medical form, the Diabetes Self-efficacy Outcomes Expectancy Questionnaire (DSEQ), the Diabetes Locus of Control Scale, and the Medical Outcomes–Short Form 36 (SF-36). A venous blood sample was taken following the interview. Data were analyzed for the total sample and separately for age groups. Results Scores on the self efficacy (DSEQ) and the locus of control (LOC) were above average for all 3 groups. Significant correlations were found among subscales of the LOC, SF-36, and HbA1c. HbA1c scores were abnormally high across groups. Significant group differences were found in duration of diabetes and number of medications used. Conclusions Despite high levels of internal locus of control and self-efficacy and scores indicating good mental, physical, emotional, and social health, self-management amongthe women was inadequate, as indicated by abnormally high HbA1c levels.
Fatigue Behavior of Porous Ti-6Al-4V Made by Laser-Engineered Net Shaping

The fatigue behavior and fracture mechanisms of additively manufactured Ti-6Al-4V specimens are investigated in this study. Three sets of testing samples were fabricated for the assessment of fatigue life. The first batch of samples was built by using Laser-Engineered Net Shaping (LENS) technology, a Direct Energy Deposition (DED) method. Internal voids and defects were induced in a second batch of samples by changing LENS machine processing parameters. Fatigue performance of these samples is compared to the wrought Ti-6Al-4V samples. The effects of machine-induced porosity are assessed on mechanical properties and results are presented in the form of SN curves for the three sets of samples. Fracture mechanisms are examined by using Scanning Electron Microscopy (SEM) to characterize the morphological characteristics of the failure surface. Different fracture surface morphologies are observed for porous and non-porous specimens due to the combination of head write speed and laser power. Formation of defects such as pores, unmelted regions, and gas entrapments affect the failure mechanisms in porous specimens. Non-porous specimens exhibit fatigue properties comparable with that of the wrought specimens, but porous specimens are found to show a tremendous reduced fatigue strength.
From good to great: the potential for the Health Care Home model to improve primary health care quality in New Zealand.

it’s 8.15am on monday morning and you have been feeling miserable since Sunday midday. You pick up the phone to get an urgent appointment with your GP. The phone rings and rings. You hold on and eventually the receptionist answers – you can hear her asking the patient in front of her to wait a moment. You ask for an urgent appointment, but your GP is booked up. You can book in to see a different GP, or wait two days. You really want to talk to your GP because it may be related to the problem you had last week. But it’s not going to happen. Since you are going to have to tell the story again anyway, you decide to go to your local emergency department instead.
Liver Stiffness Measurement and Biochemical Markers in Senegalese Chronic Hepatitis B Patients with Normal ALT and High Viral Load

Background and Aims Despite the high prevalence of chronic hepatitis B (CHB) in Africa, few studies have been performed among African patients. We sought to evaluate liver stiffness measurement by FibroScan® (LSM) and two biochemical scores (FibroTest®, Fibrometer®) to diagnose liver fibrosis in Senegalese CHB patients with HBV plasma DNA load ≥3.2 log10 IU/mL and normal alanine aminotransferase (ALT) values. Methods LSM and liver fibrosis biochemical markers were performed on 225 consecutive HBV infected Senegalese patients with high viral load. Patients with an LSM range between 7 and 13 kPa underwent liver biopsy (LB). Two experienced liver pathologists performed histological grading using Metavir and Ishak scoring. Results 225 patients were evaluated (84% male) and LB was performed in 69 patients, showing F2 and F3 fibrosis in 17% and 10% respectively. In these patients with a 7–13 kPa range of LSM, accuracy for diagnosis of significant fibrosis according to LB was unsatisfactory for all non-invasive markers with AUROCs below 0.70. For patients with LSM values below 7 kPa, FibroTest® (FT), and Fibrometer® (FM) using the cut-offs recommended by the test promoters suggested a fibrosis in 18% of cases for FT (8% severe fibrosis) and 8% for FM. For patients with LSM values greater than 13 kPa, FT, FM suggested a possible fibrosis in 73% and 70%, respectively. Conclusion In highly replicative HBV-infected African patients with normal ALT and LSM value below 13 kPa, FibroScan®, FibroTest® or Fibrometer® were unsuitable to predict the histological liver status of fibrosis.
Tacrolimus regulates endoplasmic reticulum stress–mediated osteoclastogenesis and inflammation: In vitro and collagen‐induced arthritis mouse model

Tacrolimus is an immunosuppressive drug that inhibits the release of inflammatory cytokines involved in rheumatoid arthritis development by blocking T cell activation. “Endoplasmic reticulum stress,” an imbalance between protein folding load and capacity leading to the accumulation of unfolded proteins in the endoplasmic reticulum lumen, has been implicated in rheumatoid arthritis and other inflammatory and metabolic diseases. We aimed to investigate the effect of tacrolimus on endoplasmic reticulum stress–mediated osteoclastogenesis and inflammation and elucidate the underlying mechanisms. In vitro studies were performed using mouse bone marrow cells that were cultured with or without interleukin‐1β, thapsigargin, or tacrolimus to induce osteoclast differentiation. A mouse model of arthritis was established by immunizing mice with bovine type II collagen. Tacrolimus was orally administered to mice from day 20 to 45 following the initial immunization, and histopathological changes and expression of specific biomarkers of endoplasmic reticulum stress–mediated inflammatory signaling pathways were examined. In vitro, tacrolimus inhibited receptor activator of nuclear factor‐κB ligand‐mediated osteoclast formation augmented by interleukin‐1β, thapsigargin, or both. Furthermore, tacrolimus inhibited glucose‐regulated protein (GRP78), protein kinase R‐like endoplasmic reticulum kinase, inositol‐requiring enzyme 1 (IRE 1), and activating transcription factor 6 (ATF6) augmented by interleukin‐1β, thapsigargin, or both. Tacrolimus significantly ameliorated osteolysis and endoplasmic reticulum stress intensity in mice. Simultaneously, it reduced inflammatory cell infiltration, osteoclastogenesis, and inflammatory responses by inhibiting GRP78, IRE 1, and ATF6. These findings suggest that tacrolimus exhibits an anti‐inflammation effect in rheumatoid arthritis and might inhibit joint damage progression by inhibiting endoplasmic reticulum stress.
EFFECTS OF DIETARY ALUMINUM FROM WATER TREATMENT RESIDUALS ON PHOSPHORUS STATUS AND BONE DENSITY IN GROWING LAMBS

of Thesis Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Master of Science EFFECTS OF DIETARY ALUMINUM FROM WATER TREATMENT RESIDUALS ON PHOSPHORUS STATUS AND BONE DENSITY IN GROWING LAMBS By Rachel Van Alstyne August 2005 Chair: Lee Russell McDowell Major Department: Animal Sciences Experiments using growing feeder lambs were conducted to gather data on 1) the safety of a Al-water treatment residual (WTR) ingested in amounts to provide between 2,000 and 8,000 ppm Al, and 2) the bioavailability of Al in WTR when compared to a control (910 ppm Al from sand) and a diet containing a known bioavailable form of Al from AlCl3. The study was conducted to examine changes in performance (ADG, BW, and feed intake), tissue mineral concentrations, plasma P concentrations, bone mineral content (BMC), bone density, and apparent P absorption. At experimental termination, samples of brain, liver, kidney, heart, and bone were collected and analyzed for concentrations of Ca, P, Mg, Cu, Fe, Mn, Se, and Zn. Thirty-two wether and ten female lambs were assigned to six dietary treatments: 1) control (10% sand), 2) (9.7% sand and 0.3% AlCl3), 3) (2.5% WTR and 7.5% sand), 4) (5% WTR and 5% sand), 5) (10% WTR and 0% sand), and 6) (10% WTR, 0% sand, plus double the quantities of the mineral-vitamin premix,
Alcohol intake, ADH1B and ADH1C genotypes, and the risk of colorectal cancer by sex and subsite in the Netherlands Cohort Study

The alcohol-colorectal cancer (CRC) association may differ by sex and ADH1B and ADH1C genotypes. ADH enzymes oxidize ethanol to acetaldehyde, both of which are human carcinogens. The Netherlands Cohort Study includes 120 852 participants, aged 55-69 years at baseline (1986), and has 20.3 years follow-up (case-cohort: nsubcohort = 4774; ncases = 4597). The baseline questionnaire included questions on alcohol intake at baseline and 5 years before. Using toenail DNA, available for ~75% of the cohort, we successfully genotyped six ADH1B and six ADH1C SNPs (nsubcohort = 3897; ncases = 3558). Sex- and subsite-specific Cox hazard ratios and 95% confidence intervals for CRC were estimated comparing alcohol categories, genotypes within drinkers and alcohol categories within genotype strata. We used a dominant genetic model and adjusted for multiple testing. Alcohol intake increased CRC risk in both sexes, though in women only in the (proximal) colon when in excess of 30 g/day. In male drinkers, ADH1B rs4147536 increased (distal) colon cancer risk. In female drinkers, ADH1C rs283415 increased proximal colon cancer risk. ADH1B rs3811802 and ADH1C rs4147542 decreased CRC risk in heavy (>30 g/day) and stable drinkers (compared to 5 years before baseline), respectively. Rs3811802 and rs4147542 significantly modified the alcohol-colon cancer association in women (Pfor interaction = 0.004 and 0.02, respectively). A difference in associations between genotype strata was generally clearer in men than women. In conclusion, men showed increased CRC risks across subsites and alcohol intake levels, while only colon cancer risk was increased in women at heavy intake levels. ADH1B rs3811802 and ADH1C rs4147542 significantly modified the alcohol-colon cancer association in women.
Signal‐domain optimization metrics for MPRAGE RF pulse design in parallel transmission at 7 tesla

Standard radiofrequency pulse design strategies focus on minimizing the deviation of the flip angle from a target value, which is sufficient but not necessary for signal homogeneity. An alternative approach, based directly on the signal, here is proposed for the MPRAGE sequence, and is developed in the parallel transmission framework with the use of the kT‐points parametrization.