LLukas22/scidocs huggingface dataset:
Validation of World Health Organisation HIV/AIDS Clinical Staging in Predicting Initiation of Antiretroviral Therapy and Clinical Predictors of Low CD4 Cell Count in Uganda

INTRODUCTION
The WHO clinical guidelines for HIV/AIDS are widely used in resource limited settings to represent the gold standard of CD4 counts for antiviral therapy initiation. The utility of the WHO-defined stage 1 and 2 clinical factors used in WHO HIV/AIDS clinical staging in predicting low CD4 cell count has not been established in Uganda. Although the WHO staging has shown low sensitivity for predicting CD4<200 cells/mm(3), it has not been evaluated at for CD4 cut-offs of <250 cells/mm(3) or <350 cells/mm(3).


OBJECTIVE
To validate the World Health Organisation HIV/AIDS clinical staging in predicting initiation of antiretroviral therapy in a low-resource setting and to determine the clinical predictors of low CD4 cell count in Uganda.


RESULTS
Data was collected on 395 participants from the Joint Clinical Research Centre, of whom 242 (61.3%) were classified as in stages 1 and 2 and 262 (68%) were females. Participants had a mean age of 36.8 years (SD 8.5). We found a significant inverse correlation between the CD4 lymphocyte count and WHO clinical stages. The sensitivity the WHO clinical staging at CD4 cell count of 250 cells/mm(3) and 350 cells/mm(3) was 53.5% and 49.1% respectively. Angular cheilitis, papular pruritic eruptions and recurrent upper respiratory tract infections were found to be significant predictors of low CD4 cell count among participants in WHO stage 1 and 2.


CONCLUSION
The WHO HIV/AIDS clinical staging guidelines have a low sensitivity and about half of the participants in stages 1 and 2 would be eligible for ART initiation if they had been tested for CD4 count. Angular cheilitis and papular pruritic eruptions and recurrent upper respiratory tract infections may be used, in addition to the WHO staging, to improve sensitivity in the interim, as access to CD4 machines increases in Uganda.
On-Chip Variability Sensor Using Phase-Locked Loop for Detecting and Correcting Parametric Timing Failures

Performance variability in digital integrated circuits can largely affect parametric yield and product reliability in ultra deep submicrometer technologies. As a result, variation resilience is becoming an essential design requirement for future technology nodes, especially for timing critical applications. This paper proposes an on-chip variability sensor using phase-locked loop (PLL) to detect process, supply voltage (V DD), and temperature variations (process, voltage, and temperature variation) or even temporal reliability degradation stemming from negative bias temperature instability. Our analysis shows that control voltage (V cnt) of voltage-controlled oscillator in PLL can be used as a dynamic performance signature of an operating IC. Along with the proposed PLL-based sensor circuit, we also propose a variation-resilient system technique using adaptive body biasing (ABB). The PLL V cnt signal is efficiently transformed to an optimal body bias signal for various circuit blocks to avoid possible timing failures. Correspondingly, circuits can be designed with significantly relaxed timing constraint compared to conventional approaches, where a large amount of design resources can be wasted to take care of the worst-case situations. We demonstrated our approach on a test chip fabricated in IBM 130-nm CMOS technology. Measurement results show that the PLL-based sensor is cable of tracking various sources of circuit variations. Optimization analysis shows that 42% and 43% reduction in area and power can be obtained using our approach compared to the worst-case sizing. The proposed study refers to our previous study introduced in with major improvements in measurement results and analysis.
The psychological impact of cardiovascular screening and intervention in primary care: a problem of false reassurance? British Family Heart Study Group.

BACKGROUND
There have been many reports of the adverse psychological effects of screening. Here we discuss the results of a randomized controlled study--one of the first to address this issue.


AIM
To determine the extent to which participation in a population-based intervention programme that aims to reduce the risk of cardiovascular diseases raises concerns about health, or undermines a belief in the ability to reduce that risk.


METHOD
A randomized controlled trial involving 13 general practices in England, Wales and Scotland was conducted. Two thousand, nine hundred and eighty-four middle-aged men and women undergoing cardiovascular risk-screening and intervention, and a randomized comparison group of 3,576 men and women from the same practices, who were not offered the intervention, were compared on three outcomes: perception of current health, perceived risk of suffering a heart attack, and perceived ability to reduce the risk of suffering a heart attack.


RESULTS
We found no evidence to suggest that participation in this one-year, population-based intervention programme, to reduce the risk of cardiovascular disease raised concerns about health or risk of a heart attack; indeed, those in the intervention group were slightly more optimistic about their health. Alterations in perceptions of current health and the risk of suffering a heart attack were associated directly with true alterations in risk factors. A more noticeable effect on participants in this intervention programme was a reduction in their perceived ability to further reduce their risks of a heart attack. This was associated with a decrease in weight and with quitting smoking.


CONCLUSION
Contemporary screening and intervention programmes in primary care, aimed at reducing risk of cardiovascular disease, do not necessarily lead to raised anxiety or concern about health. A more subtle effect of screening would appear to be one of reassurance in the face of continuing, albeit reduced, risk.
Characterization of memory load in an arithmetic task using non-linear analysis of EEG signals

In this paper, we investigate non-linear analysis of electroencephalogram (EEG) signals to examine changes in working memory load during the performance of a cognitive task with varying difficulty levels. EEG signals were recorded during an arithmetic task while the induced load was varying in seven levels from very easy to extremely difficult. The EEG signals were analyzed using three different non-linear/dynamic measures; namely: correlation dimension, Hurst exponent and approximate entropy. Experimental results show that the values of the measures extracted from the delta frequency band of signals acquired from the frontal and occipital lobes of the brain vary in accordance with the task difficulty level induced. The values of the correlation dimension increased as the task difficulty increased, showing a rise in complexity of the EEG signals, while the values of the Hurst exponent and approximate entropy decreased as task difficulty increased, indicating more regularity and predictability in the signals.
CASAS: A Smart Home in a Box

The CASAS architecture facilitates the development and implementation of future smart home technologies by offering an easy-to-install lightweight design that provides smart home capabilities out of the box with no customization or training.
Epidermoid cyst of the clitoris: an unusual cause of clitoromegaly in a patient without history of previous female circumcision.

STUDY OBJECTIVE
To describe a rare cause of clitoromegaly.


SETTING
University Medical Center.


PARTICIPANTS
Patient.


INTERVENTION
Magnetic resonance imaging, surgical resection of the cyst, clitoroplasty.


RESULTS
Clitoroplasty with removal of the intradermal cyst and resolution of pain.


CONCLUSIONS
A 17-year-old immigrant female presented with clitoral pain associated with clitoromegaly. Epidermoid cysts are usually solitary, asymptomatic, slow-growing, proliferations of epidermal cells that are commonly present on the neck, scalp, face, or trunk. There have only been four reported cases of epidermoid cysts of the clitoris not associated with female genital mutilation. The cyst in this case was removed by local excision, and the patient's pain has resolved.
GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text

Motivation
Best performing named entity recognition (NER) methods for biomedical literature are based on hand-crafted features or task-specific rules, which are costly to produce and difficult to generalize to other corpora. End-to-end neural networks achieve state-of-the-art performance without hand-crafted features and task-specific knowledge in non-biomedical NER tasks. However, in the biomedical domain, using the same architecture does not yield competitive performance compared with conventional machine learning models.


Results
We propose a novel end-to-end deep learning approach for biomedical NER tasks that leverages the local contexts based on n-gram character and word embeddings via Convolutional Neural Network (CNN). We call this approach GRAM-CNN. To automatically label a word, this method uses the local information around a word. Therefore, the GRAM-CNN method does not require any specific knowledge or feature engineering and can be theoretically applied to a wide range of existing NER problems. The GRAM-CNN approach was evaluated on three well-known biomedical datasets containing different BioNER entities. It obtained an F1-score of 87.26% on the Biocreative II dataset, 87.26% on the NCBI dataset and 72.57% on the JNLPBA dataset. Those results put GRAM-CNN in the lead of the biological NER methods. To the best of our knowledge, we are the first to apply CNN based structures to BioNER problems.


Availability and implementation
The GRAM-CNN source code, datasets and pre-trained model are available online at: https://github.com/valdersoul/GRAM-CNN.


Contact
andyli@ece.ufl.edu or aconesa@ufl.edu.


Supplementary information
Supplementary data are available at Bioinformatics online.
Cell–cell interactions in synaptogenesis

Synaptogenesis is a finely organized process, intriguing in its precise temporal and spatial resolution. It occurs as the dendrite of a postsynaptic neuron and an incoming axon communicate at defined sites to establish a stable synapse together. The molecular cues that guide synaptogenesis are now beginning to be identified, and cell surface interactions at synaptic sites participate prominently in the key steps. Interactions include trans-synaptic adhesion of pre- and post-synaptic neurons but also binding to non-neuronal neighboring cells and the extracellular matrix. These signals recruit scaffolding molecules, other adhesion molecules, and neurotransmitter receptors to bring together the key components of functional synapses. Recent progress provides stimulating insights into the role of adhesion and signaling molecules in the formation and function of synaptic specializations.
Effects of three different doses of a bolus injection of gadodiamide: assessment of regional cerebral blood volume maps in a blinded reader study.

BACKGROUND AND PURPOSE
Reconstruction of first-pass bolus information to derive regional cerebral blood volume (rCBV) maps is commonly performed in many centers; however, various protocols with different doses of paramagnetic contrast injections have been reported. We evaluated the dose dependency of rCBV maps in a brain tumor population by using three different doses of gadodiamide injection to evaluate their diagnostic accuracy in blinded reader sessions.


METHODS
Eighty-three patients with intraaxial brain tumors (72 gliomas) were studied at three centers and randomized to receive a bolus injection of 0.1, 0.2, or 0.3 mmol/kg per body weight of gadodiamide. rCBV maps were generated from T2*-weighted gradient-echo echoplanar sequences at 1.5 T. Data processing was performed according to the indicator dilution theory.


RESULTS
The mean contrast-to-noise ratio (CNR) was significantly different between gadodiamide doses of 0.1 and 0.2 mmol/kg (CNR = 8.7 and 15.7) and between 0.1 and 0.3 mmol/kg (CNR = 17.7). No significant difference was found between doses of 0.2 and 0.3 mmol/kg. Sensitivity for the differentiation of benign and malignant brain tumors was 80%, 95%, and 91%, and specificity was 45%, 54%, and 43% by blinded readings at 0.1, 0.2, and 0.3 mmol/ kg, respectively, as compared with histologic findings. Nonblinded readings had a sensitivity of 83%, 100%, and 90% and a specificity of 82%, 100%, and 73% at 0.1, 0.2, and 0.3 mmol/kg, respectively.


CONCLUSION
A dose of 0.2 mmol/kg of gadodiamide is recommended for reconstruction of rCBV maps if data are acquired with the T2*-weighted protocol described.
National dissemination of supported housing in the VA: model adherence versus model modification.

OBJECTIVE
The continuing development and dissemination of emerging evidence-based practices may be facilitated by the availability of descriptive information on the actual delivery of the service, and its variability, across sites. This paper presents data on the participation of 2,925 homeless veterans in the Housing and Urban Development-Veterans Affairs Supported Housing (HUD-VASH) program at 36 sites across the country, for up to five years. While most conceptual models emphasize rapid placement, sustained intensive case management, rehabilitation services, and "permanent" housing, no program has yet presented empirical data on the actual delivery of such services over an extended period of time.


METHODS
Using extensive longitudinal data from the VA's national homeless outreach program, the Health Care for Homeless Veterans (HCHV) program, a quantitative portrait presents what happens in supported housing in a large real-world dissemination effort.


RESULTS
Program entry to HUD-VASH was generally slow with 108 days (sd = 92 days) on average passing between program entry and housing placement. Total program participation lasted 2.6 years on average (sd = 1.6 years)-just half of the possible 5 years. Service delivery became substantially less intensive over time by several measures, and three-fourths of the veterans terminated within five years, although the vast majority (82%) were housed at the time. Few veterans received rehabilitation services (6%) or employment assistance (17%) and most service delivery focused on obtaining housing.


CONCLUSIONS
These data suggest that real-world supported housing programs may not adhere to the prevalent model descriptions either because of implementation failure or because veteran needs and preferences differ from those suggested by that model.
Evaluating a specific mentoring intervention for preservice teachers of primary science

Using a two-group posttest only design, 60 final year preservice teachers (control group) and 12 final year preservice teachers (intervention group) from the same university were compared after a four-week professional experience program. The intervention group received a mentoring program for developing primary science teaching practices. The survey measured both the control group and intervention group perceptions of their mentoring in primary science across previously established mentoring factors (i.e., personal attributes, system requirements, pedagogical knowledge, modelling, and feedback). Results indicated that those in the intervention group perceived they had received more mentoring experiences on each of the five factors, and ANOVA results indicated that these differences were statistically significant for the first four of the five factors. It is argued that the specific mentoring intervention designed for developing specific aspects of primary science teaching has the potential to enhance the degree and quality of teaching experiences within a preservice teacher’s professional experiences.
Assessment of the perioperative hemodynamics and right ventricular performance of lung cancer patients using a continuous cardiac output monitoring system: comparison between video-assisted thoracic surgery and muscle-sparing thoracotomy.

PURPOSE
This prospective study was conducted to assess the influences of hemodynamics and right ventricular (RV) performance after lobectomy by video-assisted thoracic surgery (VATS) and that by muscle-sparing thoracotomy (MST) using a continuous cardiac output (CCO) monitoring system.


SUBJECTS AND METHODS
Between October 2002 and April 2004, 16 patients (VATS, 8; MST, 8) who underwent lobectomy with mediastinal lymphadenectomy were enrolled in this study. Changes in hemodynamics and RV performance were evaluated preoperatively and for 36 hours postoperatively.


RESULTS
There were significant differences in operative blood loss (BL) and postoperative maxCPK/m(2) between VATS and MST groups. Postoperative values were expressed as a percentage of the preoperative values. For 36 hours perioperatively, the mean pulmonary artery pressure (mPAP), pulmonary capillary wedge pressure (PCWP) and total pulmonary resistance index (TPRI) decreased to greater extents in the VATS group than in the MST group. There were no significant differences between the two groups in RV performance including the continuous cardiac index (CCI), RV ejection fraction (RVEF), RV end-diastolic volume index (RVEDVI) and RV stroke index (SI) postoperatively.


CONCLUSION
Considering our previous report about postoperative RV performance using the VATS procedure and posterolateral thoracotomy procedure, this study suggests that pulmonary resection using either VATS or MST could be employed as minimally invasive surgery.
An isolated perfused pig heart model for the development, validation and translation of novel cardiovascular magnetic resonance techniques

BACKGROUND
Novel cardiovascular magnetic resonance (CMR) techniques and imaging biomarkers are often validated in small animal models or empirically in patients. Direct translation of small animal CMR protocols to humans is rarely possible, while validation in humans is often difficult, slow and occasionally not possible due to ethical considerations. The aim of this study is to overcome these limitations by introducing an MR-compatible, free beating, blood-perfused, isolated pig heart model for the development of novel CMR methodology.


METHODS
6 hearts were perfused outside of the MR environment to establish preparation stability. Coronary perfusion pressure (CPP), coronary blood flow (CBF), left ventricular pressure (LVP), arterial blood gas and electrolyte composition were monitored over 4 hours. Further hearts were perfused within 3T (n = 3) and 1.5T (n = 3) clinical MR scanners, and characterised using functional (CINE), perfusion and late gadolinium enhancement (LGE) imaging. Perfusion imaging was performed globally and selectively for the right (RCA) and left coronary artery (LCA). In one heart the RCA perfusion territory was determined and compared to infarct size after coronary occlusion.


RESULTS
All physiological parameters measured remained stable and within normal ranges. The model proved amenable to CMR at both field strengths using typical clinical acquisitions. There was good agreement between the RCA perfusion territory measured by selective first pass perfusion and LGE after coronary occlusion (37% versus 36% of the LV respectively).


CONCLUSIONS
This flexible model allows imaging of cardiac function in a controllable, beating, human-sized heart using clinical MR systems. It should aid further development, validation and clinical translation of novel CMR methodologies, and imaging sequences.
Artificial Neural Network and Time Series Modeling Based Approach to Forecasting the Exchange Rate in a Multivariate Framework

Any discussion on exchange rate movements and forecasting should include explanatory variables from both the current account and the capital account of the balance of payments. In this paper, we include such factors to forecast the value of the Indian rupee vis a vis the US Dollar. Further, factors reflecting political instability and lack of mechanism for enforcement of contracts that can affect both direct foreign investment and also portfolio investment, have been incorporated. The explanatory variables chosen are the 3 month Rupee Dollar futures exchange rate (FX4), NIFTY returns (NIFTYR), Dow Jones Industrial Average returns (DJIAR), Hang Seng returns (HSR), DAX returns (DR), crude oil price (COP), CBOE VIX (CV) and India VIX (IV). To forecast the exchange rate, we have used two different classes of frameworks namely, Artificial Neural Network (ANN) based models and Time Series Econometric models. Multilayer Feed Forward Neural Network (MLFFNN) and Nonlinear Autoregressive models with Exogenous Input (NARX) Neural Network are the approaches that we have used as ANN models. Generalized Autoregressive Conditional Heteroskedastic (GARCH) and Exponential Generalized Autoregressive Conditional Heteroskedastic (EGARCH) techniques are the ones that we have used as Time Series Econometric methods. Within our framework, our results indicate that, although the two different approaches are quite efficient in forecasting the exchange rate, MLFNN and NARX are the most efficient. Journal of Insurance and Financial Management ARTICLE INFO JEL Classification: C22 C45 C63 F31 F47
Chinese Parsing Exploiting Characters

Characters play an important role in the Chinese language, yet computational processing of Chinese has been dominated by word-based approaches, with leaves in syntax trees being words. We investigate Chinese parsing from the character-level, extending the notion of phrase-structure trees by annotating internal structures of words. We demonstrate the importance of character-level information to Chinese processing by building a joint segmentation, part-of-speech (POS) tagging and phrase-structure parsing system that integrates character-structure features. Our joint system significantly outperforms a state-of-the-art word-based baseline on the standard CTB5 test, and gives the best published results for Chinese parsing.
Thalidomide with peginterferon alfa-2b and ribavirin in the treatment of non-responders genotype 1 chronic hepatitis C patients: proof of concept.

BACKGROUND
fewer than half of patients infected with hepatitis C virus (HCV) achieve sustained viral clearance after peginterferon alfa/ribavirin (Peg-IFN/RBV) therapy.


AIMS
thalidomide posses anti-inflammatory and immunomodulatory properties through inhibition of tumor necrosis factor and costimulatory effect on human CD8+ T cells.


METHODS
we started a prospective, open label trial of retreatment of very-difficult-to-treat genotype 1 chronic hepatitis C patients (CHC) patients, who had failed to respond to the (Peg-IFN/RBV), with a triple therapy consisting in these same antivirals plus thalidomide 200 mg/day (the TRITAL study).


RESULTS
none of the eleven patients fulfilling the inclusion criteria and included in the trial reached complete early virological response or sustained virological response. Viral load decline after 12 weeks of triple therapy thalidomide-based retreatment did not differ from viral dynamics during the first course. The triple therapy was well tolerated and only one patient developed mild bilateral neuropathy.


CONCLUSIONS
thalidomide addition to standard therapy is tolerated and did not increase the SVR rate in very-difficult-to-treat genotype 1 CHC patients. Different schedules are warranted to improve attempting retreatment of non responder CHC patients.