ahmedabdelwahed/Medical_papers_title_and_abstract_NLP_dataset huggingface dataset:
Towards a new horizon of optoelectronic devices with liquid crystals

The liquid crystal having high viscosity is attracting increasing attention as a new type of quality organic semiconductor, i.e., self-organizing molecular semiconductor In this article, its state-and-the-art in materials, properties related to charge carrier transport, and device applications, is reviewed briefly. In addition, the further researches needed towards its practical applications are discussed.
Charge-Redistribution Based Quadratic Operators for Neural Feature Extraction

This paper presents a SAR converter based mixed-signal multiplier for the feature extraction of neural signals using quadratic operators. After a thorough analysis of design principles and circuit-level aspects, the proposed architecture is explored for the implementation of two quadratic operators often used for the characterization of neural activity, the moving average energy (MAE) operator and the nonlinear energy operator (NEO). Programmable chips for both operators have been implemented in a HV-180 nm CMOS process. Experimental results confirm their suitability for energy computation and action potential detection and the accomplished areaxpower performance is compared to prior art. The MAE and NEO prototypes, at a sampling rate of 30kS/s, consume 116 nW and 178 nW, respectively, and digitize both the input neural signal and the operator outcome, with no need for digital multipliers.
New microstrip elliptic function bandpass filters using the edge-coupled folded split ring resonators

In this paper, new microstrip cross-coupled elliptic,function (CCEF) bandpass filters (BPFs) using folded split-ring resonators (FSRR) art proposed. The CCEF BPFs using these resonators are designed with maintaining a good filter performance and reducing the size significantly. The four-pole and three-pole CCEF BPFs show a 3-dB bandwidth of 3.0% at the center-frequency of 2.0 GHz, and insertion losses of 4.28 and 2.77 dB, respectively. (c) 2006 Wiley Periodicals, Inc.
Silicon Nitride Nanopores Formed by Simple Chemical Etching: DNA Translocations and TEM Imaging

We demonstrate DNA translocations through silicon nitride pores formed by simple chemical etching on glass substrates using microscopic amounts of hydrofluoric acid. DNA translocations and transmission electron microscopy (TEM) prove the fabrication of nanopores and allow their characterization. From ionic measurements on 318 chips, we report the effective pore diameters ranging from zero (pristine membranes) and sub-nm to over 100 nm, within 50 μm diameter membranes. The combination of ionic conductance, DNA current blockades, TEM imaging, and electron energy loss spectroscopy (EELS) provides comprehensive information about the pore area and number, from single to few pores, and pore structure. We also show the formation of thinned membrane regions as precursors of pores. The average pore density, about 5 × 10-4 pores/μm2, allows pore number adjustment statistically (0, 1, or more). This simple and affordable chemical method for making solid-state nanopores accelerates their adoption for DNA sensing and characterization applications.
Gaviss : Boosting the Performance of GPU-Accelerated NFV Systems via Data Sharing

GPUs have demonstrated the capability of significantly improving the performance of network functions (NF). In an Network Function Virtualization (NFV) system, multiple NFs form a service chain to provide services. However, NFs in state-of-the-art GPU-accelerated NFV systems still utilize a GPU independently where each NF needs to transfer data to the GPU memory for acceleration. As a result, a packet might be transferred into the GPU memory by each NF when it passes through the service chain. We find these expensive and repetitive transfers are the main factor that limits the overall performance of an NFV system. We propose Gaviss, a GPU-accelerated NFV system with effective data sharing. By sharing packets in the GPU memory among network functions, a packet needs to be transferred to the GPU only once, eliminating the performance overhead caused by repetitive transfers. Extensive experimental results show that Gaviss can improve the overall throughput by 2.6-13.2x and reduce the latency by up to 37.9%, when compared with state-of-the-art approaches. Moreover, Gaviss also demonstrates up to 2.5x higher price-performance ratio than CPU-based implementations, making GPUs competitive for building NFV systems.
GLISTR: Glioma Image Segmentation and Registration

We present a generative approach for simultaneously registering a probabilistic atlas of a healthy population to brain magnetic resonance (MR) scans showing glioma and segmenting the scans into tumor as well as healthy tissue labels. The proposed method is based on the expectation maximization (EM) algorithm that incorporates a glioma growth model for atlas seeding, a process which modifies the original atlas into one with tumor and edema adapted to best match a given set of patient's images. The modified atlas is registered into the patient space and utilized for estimating the posterior probabilities of various tissue labels. EM iteratively refines the estimates of the posterior probabilities of tissue labels, the deformation field and the tumor growth model parameters. Hence, in addition to segmentation, the proposed method results in atlas registration and a low-dimensional description of the patient scans through estimation of tumor model parameters. We validate the method by automatically segmenting 10 MR scans and comparing the results to those produced by clinical experts and two state-of-the-art methods. The resulting segmentations of tumor and edema outperform the results of the reference methods, and achieve a similar accuracy from a second human rater. We additionally apply the method to 122 patients scans and report the estimated tumor model parameters and their relations with segmentation and registration results. Based on the results from this patient population, we construct a statistical atlas of the glioma by inverting the estimated deformation fields to warp the tumor segmentations of patients scans into a common space.
Epidemiological profile, spatial patterns and priority areas for surveillance and control of leishmaniasis in Brazilian border strip, 2009-2017

Leishmaniasis represents a major neglected public health problem and the control measures have not been successful in Brazil. Recent studies have shown leishmaniasis importance to Brazilian border zones which reinforces the need to investigate its spread in those regions. This study aimed to analyze epidemiologic profile and its spatial distribution or aggregation process in both tegumentary and visceral leishmaniasis in the Brazilian border strip from 2009 to 2017. This is an ecological study of the epidemiological profile and spatial patterns encompassing municipalities in the Brazilian border strip. The presence of spatial autocorrelation and determination of priority areas for disease control were performed using global (Moran I) and local (LISA) Moran spatial techniques. The annual mean coefficients of tegumentary and visceral leishmaniasis were 29.8 and 0.6 by 100,000 inhabitants in the border strip, respectively. The indigenous population rates of leishmaniasis in the border zone appears to be higher than in the rest of the country (cutaneous changed from 33.2% to 6.6% and visceral rising from 1.0% to 17.5%) in the period. The most affected municipalities were located in the North and Central arches of the border zone. The results can subsidize the development of more targeted and effective strategies that can contribute to the surveillance and control of leishmaniasis in border zones, as the provision of epidemiological and spatial data on the disease. For better control of the disease, we recommend and emphasize the need to integrate public health policies of neighboring countries.
Segmented MS/MS acquisition of a1 ion-based strategy for in-depth proteome quantitation

In-depth proteome quantitation is of great significance for understanding protein functions, advancing biological, medical, environmental and metabolic engineering research. Herein, benefiting from the high formation efficiencies and intensities of dimethyl-labeled a1 ions for accurate quantitation, we developed an in-depth a1 ion-based proteome quantitation method, named deep-APQ, by a sequential MS/MS acquisition of the high mass range for identification and the low mass range for a1 ion intensity extraction to increase quantitative protein number and sequence coverage. By the analysis of HeLa protein digests, our developed method showed deeper quantitative coverage than our previously reported a1 ion-based quantitation method without mass range segmentation and lower missing values than widely-used label-free quantitation method. It also exhibited excellent accuracy and precision within a 20-fold dynamic range. We further integrated a workflow combining the deep-APQ method with highly efficient sample preparation, high-pH and low-pH reversed-phase separation and high-field asymmetric waveform ion mobility spectrometry (FAIMS) to study E. coli proteome responses under the nutritional conditions of glucose and acetate. A total of 3447 proteins were quantified, representing 82% of protein-coding genes, with the average sequence coverage up to 40%, demonstrating the high coverage of quantitation results. We found that most of the quantified proteins related to chemotaxis were differentially expressed, including the low-abundance proteins such as tap, trg, aer, cheA and cheB, indicating that chemotaxis would play an important role for E. coli cell to survive from acetate toxicity. The above results demonstrated that the deep-APQ method is of great promising to achieve the deep-coverage proteome quantitation with high confidence.
Coerced Abortion - The Neglected Face of Reproductive Coercion

Reproductive coercion encompasses a collection of pregnancy promoting and pregnancy avoiding behaviours. Coercion may vary in severity and be perpetrated by intimate partners or others. Research is complicated by the inclusion of behaviours that do not necessarily involve an intention to influence reproduction, such as contraceptive sabotage. These behaviours are the most common, but are not always included in survey instruments. This may explain why the prevalence of reproductive coercion varies widely. Prevalence also varies when coerced abortion is included in survey instruments. When it is, it seems roughly comparable in prevalence to coercion intended to impregnate. The extent and nature of coerced abortion can also be derived from studies that explore the reasons why women access abortion, the relationship between abortion and intimate partner violence, and online blogs and forums. This narrative review of reproductive coercion examines the evidence and attempts to comprehend why coerced abortion has been neglected.
Multi-Scale Segmentation and Surface Fitting for Measuring 3-D Macular Holes

Macular holes are blinding conditions, where a hole develops in the central part of retina, resulting in reduced central vision. The prognosis and treatment options are related to a number of variables, including the macular hole size and shape. High-resolution spectral domain optical coherence tomography allows precise imaging of the macular hole geometry in three dimensions, but the measurement of these by human observers is time-consuming and prone to high inter-and intra-observer variability, being characteristically measured in 2-D rather than 3-D. We introduce several novel techniques to automatically retrieve accurate 3-D measurements of the macular hole, including: surface area, base area, base diameter, top area, top diameter, height, and minimum diameter. Specifically, we introduce a multi-scale 3-D level set segmentation approach based on a state-of-the-art level set method, and we introduce novel curvature-based cutting and 3-D measurement procedures. The algorithm is fully automatic, and we validate our extracted measurements both qualitatively and quantitatively, where our results show the method to be robust across a variety of scenarios. Our automated processes are considered a significant contribution for clinical applications.
The Complex Process of Using the Interconnected Knee Arthroplasty Device Clearance Pathway

Background: The clearance of medical devices by the US Food and Drug Administration (FDA) has remained largely unchanged since 1976, when the Medical Device Amendments Act established a system classifying devices into 3 categories based on safety risk to the consumer. The system allows for the clearance of many orthopedics devices through the 510(k) premarket pathway, which is based on "predicate ancestors," previously cleared devices that are "substantially equivalent." Purpose: We sought to trace the predicate ancestors of modern total knee arthroplasty (TKA) devices, specifically those recently cleared for marketing by the 510(k) pathway that claim substantial equivalence to prior devices, despite potential differences in material science and design. In addition, we aimed to document which TKA devices cleared by the 510(k) pathway have substantial equivalence to devices that have since been recalled by the FDA. Methods: To create a comprehensive list of TKA devices, we used FDA Classification Process Codes corresponding to knee arthroplasty to search the FDA's databases from May 28, 1976, the start of the 510(k) process, to May 1, 2021. Of 1309 resulting devices, 89 were excluded as not related to arthroplasty. For each of the remaining devices, we analyzed the descendant devices that claimed substantial equivalence, either directly or indirectly. We used data of recalled designs to determine both the absolute number of recalled devices and the number of currently cleared devices that presented substantial equivalence claims upon predicates that have since been recalled. Results: Of 1220 knee devices cleared or approved, 6 (0.5%) were approved through the premarket approval application (PMA) process, and 1214 (99.5%) were cleared through the 510(k) pathway. Of the 1214 cleared devices, 217 (17.9%) have been recalled and 204 (16.8%) have ties to at least 1 recalled predicate device linked through generational claims of substantial equivalence. We found 90 devices (7.4%) linked directly to a recalled predicate device. Conclusions: Most knee arthroplasty devices are cleared for marketing through reliance on a complex web of equivalency to previously cleared predicates. We found that many TKA devices thus connected were cleared decades apart, with multiple iterations of design and material modifications. Many currently marketed TKA devices have claimed equivalency to predicates that have been recalled. Our findings suggest the need for novel regulatory strategies that might further patient safety while balancing the unwanted effects of regulatory burden.
Edge-Preserving PET Image Reconstruction Using Trust Optimization Transfer

Iterative image reconstruction for positron emission tomography can improve image quality by using spatial regularization. The most commonly used quadratic penalty often oversmoothes sharp edges and fine features in reconstructed images, while nonquadratic penalties can preserve edges and achieve higher contrast recovery. Existing optimization algorithms such as the expectation maximization (EM) and preconditioned conjugate gradient (PCG) algorithms work well for the quadratic penalty, but are less efficient for high-curvature or nonsmooth edge-preserving regularizations. This paper proposes a new algorithm to accelerate edge-preserving image reconstruction by using two strategies: trust surrogate and optimization transfer descent. Trust surrogate approximates the original penalty by a smoother function at each iteration, but guarantees the algorithm to descend monotonically; Optimization transfer descent accelerates a conventional optimization transfer algorithm by using conjugate gradient and line search. Results of computer simulations and real 3-D data show that the proposed algorithm converges much faster than the conventional EM and PCG for smooth edge-preserving regularization and can also be more efficient than the current state-of-art algorithms for the nonsmooth l(1) regularization.
Coping with a lack of evidence: living-donor kidney transplantation in the initial phase of the SARS-CoV-2 pandemic

Due to immunosuppressive therapy, transplant patients are more susceptible to viral and bacterial infections. A potentially deadly new virus haunted us in 2020: SARS-CoV‑2, causing coronavirus disease 19 (COVID-19). We analyzed the consequences of this previously unknown risk for our living-donor transplant program in the first year of the pandemic. After the complete lockdown in spring 2020, our transplant center in Linz resumed the living-donor kidney transplantation program from June to September 2020, between the first and second waves of COVID-19 in Austria. We compared the outcomes of these living-donor kidney transplantations with the transplant outcomes of the corresponding periods of the three previous years. From June 4 to September 9, 2020, five living-donor kidney transplantations were performed. All donors and recipients were screened for COVID 19 infection by PCR testing the day before surgery. Kidney transplant recipients remained isolated in single rooms until discharge from hospital. All recipients and donors remained SARS-CoV‑2 negative during the follow-up of 10 months and have been fully vaccinated to date. The number of living transplants in the studied period of 2020 was constant compared to the same months of 2017, 2018, and 2019. Living-donor kidney transplantation can be continued using testing for SARS-CoV‑2 and meticulous hygienic precautions in epidemiologically favorable phases of the SARS-CoV‑2 pandemic. Donors and recipients should be carefully selected and informed about risks and benefits.
Complete mitochondrial genome of the American flamingo, Phoenicopterus ruber (Phoenicopteriformes, Phoenicopteridae)

The American flamingo, Phoenicopterus ruber (P. ruber), is a large species of flamingo closely related to the greater flamingo and Chilean flamingo. In this paper, the complete mitochondrial genome sequence of P. ruber has been assembled for the first time. It was 17 476 bp in length and consisted of 13 typical vertebrate protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 control regions. COI and ND3 genes used GTG and ATC as start codons respectively, but the remaining protein-coding genes were encoded beginning with orthodox ATG codon. Two triplet codons (TAA, AGG) and one single T base were employed as stop codons. The arrangement of the overall genes and noncoding regions was identical to the same genus flamingo Phoenicopterus roseus. The AT content (54.27%) was higher than the GC content. Phylogenetic analysis was performed using 12 protein-coding genes, combined with other 11 species from the same Neognathae, which validated the responsibility and utility of this new mitochondrial genome.
Cell Envelope Stress Response in Pseudomonas aeruginosa

Bacteria sense their environment via the cell envelope, which in Gram-negative bacteria comprises the outer membrane, the periplasmic space, and the inner membrane. Pseudomonas aeruginosa is an opportunistic pathogen which is exposed to different cell wall stresses imposed by exposure to antibiotics, osmotic pressure, and long-time colonization of host tissues such as the lung in cystic fibrosis patients. In response to these stresses, P. aeruginosa is able to respond by establishing a cell envelope stress response involving different regulatory pathways including the extra-cytoplasmic sigma factors AlgU, SigX, and SbrI and other two-component sensor/response regulators and effectors. This chapter aims to review the different factors leading to the activation of the cell envelope stress response in P. aeruginosa and the genetic determinants involved in this response, which is crucial for the survival of the bacterium upon exposure to different stressful conditions.
IgE type multiple myeloma exhibits hypermutated phenotype and tumor reactive T cells

Multiple myeloma (MM) is a hematological malignancy originating from malignant and clonally expanding plasma cells. MM can be molecularly stratified, and its clonal evolution deciphered based on the Ig heavy and light chains of the respective malignant plasma cell clone. Of all MM subtypes, IgE type MM accounts for only &lt;0.1% of cases and is associated with an aggressive clinical course and consequentially dismal prognosis. In such malignancies, adoptive transfer of autologous lymphocytes specifically targeting presented (neo)epitopes encoded by either somatically mutated or specifically overexpressed genes has resulted in substantial objective clinical regressions even in relapsed/refractory disease. However, there are no data on the genetic and immunological characteristics of this rare and aggressive entity. Here, we comprehensively profiled IgE type kappa MM on a genomic and immune repertoire level by integrating DNA- and single-cell RNA sequencing and comparative profiling against non-IgE type MM samples. We demonstrate distinct pathophysiological mechanisms as well as novel opportunities for targeting IgE type MM. Our data further provides the rationale for patient-individualized neoepitope-targeting cell therapy in high tumor mutation burden MM.
Deep mutational scanning and massively parallel kinetics of plasminogen activator inhibitor-1 functional stability to probe its latency transition

Plasminogen activator inhibitor-1 (PAI-1), a member of the serine protease inhibitor superfamily of proteins, is unique among serine protease inhibitors for exhibiting a spontaneous conformational change to a latent or inactive state. The functional half-life for this transition at physiologic temperature and pH is ∼1 to 2 h. To better understand the molecular mechanisms underlying this transition, we now report on the analysis of a comprehensive PAI-1 variant library expressed on filamentous phage and selected for functional stability after 48 h at 37 °C. Of the 7201 possible single amino acid substitutions in PAI-1, we identified 439 that increased the functional stability of PAI-1 beyond that of the WT protein. We also found 1549 single amino acid substitutions that retained inhibitory activity toward the canonical target protease of PAI-1 (urokinase-like plasminogen activator), whereas exhibiting functional stability less than or equal to that of WT PAI-1. Missense mutations that increase PAI-1 functional stability are concentrated in highly flexible regions within the PAI-1 structure. Finally, we developed a method for simultaneously measuring the functional half-lives of hundreds of PAI-1 variants in a multiplexed, massively parallel manner, quantifying the functional half-lives for 697 single missense variants of PAI-1 by this approach. Overall, these findings provide novel insight into the mechanisms underlying the latency transition of PAI-1 and provide a database for interpreting human PAI-1 genetic variants.
Barrier height tuning in Ti/4H-SiC Schottky diodes

In this work, we investigated the effects of annealing temperature and metal thickness on the Schottky barrier height in state-of-the-art Ti/4H-SiC rectifiers. By varying these two parameters, a controlled lowering of the Schottky barrier height has been obtained, thus giving the possibility to improve the efficiency of device in terms of power consumption.