ahmedabdelwahed/Medical_papers_title_and_abstract_NLP_dataset huggingface dataset:
Investigating Physiopathological Roles for Sirtuins in a Mouse Model

Sirtuins are identified as NAD+-dependent class III histone deacetylases (HDAC) and are involved in a variety of cellular activities, including energy metabolism, DNA repair, epigenetics, gene expression, cell proliferation, differentiation, and survival. Using genetically modified model organisms, sirtuins are proved to be one of the most conserved aging-regulatory and longevity-promoting genes/pathways among species. Of the seven sirtuins, SIRT7 is the only sirtuin that localizes in the nucleolus. SIRT7 senses endogenous and environmental stress to maintain physiological homeostasis. Sirt7 deficient and transgenic mice provide a useful tool to understand the mechanisms of aging and related pathologies. In this chapter, we summarized the most widely applied methods to understand the physiopathological function of SIRT7 in mice.
Fundamentals of HDX-MS

Hydrogen deuterium exchange mass spectrometry (HDX-MS) is becoming part of the standard repertoire of techniques used by molecular biologists to investigate protein structure and dynamics. This is partly due to the increased use of automation in all stages of the technique and its versatility of application-many proteins that present challenges with techniques such as X-ray crystallography and cryoelectron microscopy are amenable to investigation with HDX-MS. The present review is aimed at scientists who are curious about the technique, and how it may aid their research. It describes the fundamental basis of solvent exchange, the basics of a standard HDX-MS experiment, as well as highlighting emerging novel experimental advances, which point to where the field is heading.
Molecular hydrogen positively influences lateral root formation by regulating hydrogen peroxide signaling

Although a previous study discovered that exogenous molecular hydrogen (H2) supplied with hydrogen-rich water (HRW) can mediate lateral root (LR) development, whether or how endogenous H2 influences LR formation is still elusive. In this report, mimicking the induction responses in tomato seedlings achieved by HRW or exogenous hydrogen peroxide (H2O2; a positive control), transgenic Arabidopsis that overexpressed the hydrogenase1 gene (CrHYD1) from Chlamydomonas reinhardtii not only stimulated endogenous hydrogen peroxide (H2O2) production, but also markedly promoted LR formation. Above H2 and H2O2 responses were abolished by the removal of endogenous H2O2. Moreover, the changes in transcriptional patterns of representative cell cycle genes and auxin signaling-related genes during LR development in both tomato and transgenic Arabidopsis thaliana matched with above phenotypes. The alternations in the levels of GUS transcripts driven by the CYCB1 promoter and expression of PIN1 protein further indicated that H2O2 synthesis was tightly linked to LR formation achieved by endogenous H2, and cell cycle regulation and auxin-dependent pathway might be their targets. There results might provide a reference for molecular mechanism underlying the regulation of root morphogenesis by H2.
Efficient Scheduling for the Massive Random Access Gaussian Channel

This article investigates the massive random access Gaussian channel with a focus on small payloads. For this problem, grant-based schemes have been regarded as inefficient due to the necessity of large feedbacks and the use of inefficient scheduling request methods. This articles attempts to answer whether grant-based schemes can be competitive against state-ot-art grantless schemes and worthy of further investigation. In order to compare these schemes fairly, a novel model is proposed, and, under this model, a novel grant-based scheme is proposed. The scheme uses Ordentlich and Polyanskiy's grantless method to transmit small coordination indices in order to perform the scheduling request, which allows both the request from the users to be efficient and the feedback to be small. We also present improvements to the Ordentlich and Polyanskiy's scheme, allowing it to transmit information through the choice of sub-block, as well as to handle collisions of the same message, significantly improving the method for very small messages. Simulation results show that, if a small feedback is allowed, the proposed scheme performs closely to the state-of-art while using simpler coding schemes, suggesting that novel grant-based schemes should not be dismissed as a potential solution to the massive random access problem.
A Novel SCA-Based Method for Beamforming Optimization in IRS/RIS-Assisted MU-MISO Downlink

In this letter, we consider the fundamental problem of jointly designing the transmit beamformers and the phase shifts of the intelligent reflecting surface (IRS)/reconfigurable intelligent surface (RIS) to minimize the transmit power, subject to quality-of-service constraints at individual users in an IRS-assisted multiuser multiple-input single-output downlink communication system. In particular, we propose a new successive convex approximation based second-order cone programming approach in which all the optimization variables are simultaneously updated in each iteration. Our proposed scheme achieves superior performance compared to state-of-the-art benchmark solutions. In addition, the complexity of the proposed scheme is O(N-s(3.5)), while that of state-of-the-art benchmark schemes is O(N-s(7)), where Ns denotes the number of reflecting elements at the IRS.
Expression and Crystallization of HDAC6 Tandem Catalytic Domains

Histone deacetylase 6 (HDAC6) is an atypical lysine deacetylase with tandem catalytic domains and an ubiquitin-binding zinc finger domain. HDAC6 is involved in various biological processes, such as cell motility or stress responses, and has been implicated in pathologies ranging from cancer to neurodegeneration. Due to this broad range of functions, there has been considerable interest in developing HDAC6-specific small molecule inhibitors, several of which are already available. The crystal structure of the tandem catalytic domains of zebrafish HDAC6 has revealed an arrangement with twofold symmetry and extensive surface interaction between the catalytic domains. Further dissection of the biochemical properties of HDAC6 and the development of novel inhibitors will benefit from being able to routinely express high-quality protein. We present here our optimized protocol for expression and crystallization of the zebrafish tandem catalytic domains.
Perspective-SIFT: An efficient tool for low-altitude remote sensing image registration

This paper presents an automated image registration approach that is robust to perspective distortions. State-of-the-art method affine-SIFT uses affine transform to simulate various viewpoints to increase the robustness of registration. However, affine transformation does not follow the process by which real-world images are formed. To solve this problem, we propose a perspective scale invariant feature transform (PSIFT) that uses homographic transformation to simulate perspective distortion. As for ASIFT, PSIFT is based on the scale invariant feature transform (SIFT) and has a two-resolution scheme, namely a low-resolution phase and a high-resolution phase. The low-resolution phase of PSIFT simulates several image views following a perspective transformation by varying two camera axis orientation parameters. Given those simulated images, SIFT is then used to extract features and find matches among them. In the high-resolution phase, the perspective transformations which lead the largest number of matches in the low-resolution stage are selected to generate SIFT features on the original images. Experimental results obtained on three categories of low-altitude remote sensing images and Morel-Yu's dataset show that PSIFT outperforms significantly the state-of-the-art ASIFT, SIFT, Random Ferns, Harris-Affine, MSER and Hessian Affine, especially when images suffer severe perspective distortion. (C) 2013 Elsevier B.V. All rights reserved.
Phase-Transition-Cycle-Induced Recrystallization of FAPbI3 Film in An Open Environment Toward Excellent Photodetectors with High Reproducibility

Perovskite is an attractive building block for future optoelectronic applications. However, the strict fabrication conditions of perovskite devices impede the transformation of lab techniques into commercial applications. Here, a facile annealing-free posttreatment is proposed to reconstruct the perovskite film to obtain high-performance photodetectors with an optimized production rate. With posttreatment by methylamine thiocyanate, the prefabricated formamidinium-lead triiodide (FAPbI3 ) film will undergo a recrystallization process consisting of a repeating phase-transition-cycle (PTC) between the black and yellow phases of FAPbI3 , which improves the crystal quality and eliminates defects. As a result, some casually prepared or even decomposed perovskite films can be reconstructed, and the dispersion degree of the device performance based on the posttreatment method decreases by ≈21% compared to the traditional antisolvent method. This facile and annealing-free posttreatment will be an attractive method for the future industrial production of perovskite devices.
The Predictive Utility of Trauma Subtypes in the Assessment of Mental Health Outcomes for Persons Resettled as Refugees

Pre-migration trauma, a psychological risk factor for refugees, is often measured using cumulative indices. However, recent research suggests that trauma subtypes, rather than cumulative trauma, may better predict psychological outcomes. This study investigated the predictive utility of trauma subtypes in the assessment of refugee mental health. Multiple regression was used to determine whether cumulative trauma or trauma subtypes explained more variance in depression, anxiety, and post-traumatic stress disorder (PTSD) symptom scores in 70 Syrian and Iraqi refugees. Subtype models performed better than cumulative trauma models for PTSD (cumulative R2 = 0.138; subtype R2 = 0.32), anxiety (cumulative R2 = 0.061; subtype R2 = 0.246), and depression (cumulative R2 = 0.041; subtype R2 = 0.184). Victimization was the only subtype significantly associated with PTSD (p < 0.001; r2 = 0.210), anxiety (p < 0.001; r2 = 0.162), and depression (p = 0.002; r2 = 0.140). Cumulative trauma was predictive of PTSD symptoms only (p = 0.003; r2 = 0.125). Trauma subtypes were more informative than cumulative trauma, indicating their utility for improving predictive efforts in research and clinical contexts.
Cultural Sustainability of US Cities: The Scaling of Non-Profit Arts Footprint with Population

The functional characteristics of urban systems vary predictably with Metropolitan Statistical Area (MSA) population, with certain metrics increasing apace with population (e.g., housing stock), some increasing faster than population (e.g., wealth), and others increasing slower than population (infrastructure elements). Culture has been designated the fourth pillar of sustainability. The population-dependent scaling of operating revenue, work space, and number of employees was investigated for almost 3000 arts organizations in the US, both in aggregate and by arts discipline (music, theater, visual and design arts, dance, and museums). Unlike general measures of creativity, the three measures of economic footprint did not scale supra-linearly with the population of metropolitan areas. Rather, operating revenue scaled linearly (e.g., like amenities), and work space and employee number scaled sub-linearly (e.g., like infrastructure). The cost of living, proxied by housing costs, increased with MSA population, though not as rapidly as did arts organization operating revenue, indicating a degree of uncoupling. The generally higher educational attainment of adults in larger cities, coupled with the growth of the education-dependent arts patronage, suggest a funding focus on less populous (50,000-1,000,000), as well as on under-performing, cities.
Suspect face retrieval system using multicriteria decision process and deep learning

The identification and apprehending of suspects by law enforcement authorities rely heavily on facial sketches. The sketch artist creates sketches based on the witnesses' memories. Sketch artists are few and limited in their availability. It is also evident that as time passes, the eyewitness forgets many of the important details, which can be expensive in time-sensitive investigations. The sketch was used to obtain the suspect's image through the state-of-the-art sketch-photo retrieval model, which missed the relevance of time sensitivity. A linguistic description-based suspect face image retrieval approach is presented in this study. In the proposed approach, the facial attribute-value pair is extracted from eyewitness descriptions. Facial attribute saliency is also studied in this work and validated with the Fuzzy Analytic Hierarchy Process (FAHP) model. A weighted score is computed to retrieve the suspect face images. The effectiveness of the proposed method is assessed by comparing it to existing linguistic sketch-based retrieval methods as well as the sketch to photo retrieval models. As compared to state-of-the-art approaches, experimental results give an accuracy of 94.98%.
Inter-domain routing for communication networks using Hierarchical Hopfield Neural Networks

This paper presents the Hierarchical Hopfield Neural Networks (HHNN). HHNN is a novel Hopfield Neural Network (HNN) approach. HHNN is composed of a hierarchy of self-sufficient HNNs, aiming to reduce the neural network structure and mitigate convergence problems. The HNNN composition depends on the applied problem. In this paper, the problem approached is the inter-domain routing for communication networks. Thus, the hierarchy of HNNs mimics the structure of communication networks (domains, nodes, and links). The proof of concept and the comparison between HNNN with the state-of-art HNN occurs using an implementation of them in the Java programming language. Besides, the performance analysis of the HHNN runs on a parallel hardware platform, using VHDL to develop it. The results have demonstrated a reduction of 93.75% and 99.98% in the number of neurons and connections to build the neural network, respectively. Furthermore, the mean time to achieve convergence of HHNN is rough 1.52% of the total time needed by the current state-of-art HNN approach. It is also less susceptible to early convergence problems when used in communications networks with a large number of nodes. Last, but not least, the VHDL implementation shows that convergence time of HHNN is comparable to routing algorithms used in practical applications.
Analysis and optimization of coplanar RLC lines for GSI global interconnection

Compact physical models are derived for the delay and crosstalk of on-chip coplanar transmission lines, which are used in state-of-the-art high-speed microprocessors. These lines are mainly used for long global interconnects that are relatively thick and wide and have prominent inductive effects. The models are then used to optimize the design of coplanar global interconnects.
Computer-aided diagnosis of mammographic masses based on a supervised content-based image retrieval approach

In this work, the incorporation of content-based image retrieval (CBIR) into computer aided diagnosis (CADx) is investigated, in order to contribute to the decision-making process of radiologists in the characterization of mammographic masses. The proposed scheme comprises two stages: A margin-specific supervised CBIR stage that retrieves images from reference cases along with a decision stage that is based on the retrieved items. The feature set utilized exploits state-of-the-art features along with a newly proposed texture descriptor, namely mHOG, targeted to capturing margin and core specific mass properties. Performance evaluation considers the CBIR and diagnosis stages separately and is addressed by using standard measures on an enhanced version of the widely adopted digital database for screening mammography (DDSM). The proposed scheme achieved improved performance of CADx of masses in X-ray mammography experimentally compared to the state-of-the-art. (C) 2017 Elsevier Ltd. All rights reserved.
Brainnetome atlas of preadolescent children based on anatomical connectivity profiles

During the preadolescent period, when the cerebral thickness, curvature, and myelin are constantly changing, the brain's regionalization patterns underwent persistent development, contributing to the continuous improvements of various higher cognitive functions. Using a brain atlas to study the development of these functions has attracted much attention. However, the brains of children do not always have the same topological patterns as those of adults. Therefore, age-specific brain mapping is particularly important, serving as a basic and indispensable tool to study the normal development of children. In this study, we took advantage of longitudinal data to create the brain atlas specifically for preadolescent children. The resulting human Child Brainnetome Atlas, with 188 cortical and 36 subcortical subregions, provides a precise period-specific and cross-validated version of the brain atlas that is more appropriate for adoption in the preadolescent period. In addition, we compared and illustrated for regions with different topological patterns in the child and adult atlases, providing a topologically consistent reference for subsequent research studying child and adolescent development.
Closing the HIV Treatment Gap for Adolescents in Windhoek, Namibia: A Retrospective Analysis of Predictors of Viral Non-Suppression

Windhoek joined the Fast-Track Cities Initiative in 2017 to optimize HIV service delivery for adolescents, promoting adherence and sustaining viral suppression. Recent surveys and programmatic data show that the treatment gap remains greatest among children and adolescents living with HIV. A retrospective cohort analysis of adolescents living with HIV (ALHIV) receiving antiretroviral therapy (ART) at Windhoek healthcare facilities was conducted. Routine clinical data were extracted from the electronic Patient Monitoring System (ePMS). The SPSS statistical package was used to determine viral non-suppression and perform inferential statistics. 695 ALHIV were analysed with median age of 16 years (IQR = 13-18). Viral non-suppression at 1000 copies/mL threshold was 12%. Viral non-suppression was associated with age at ART initiation, duration on ART, current ART regimen and WHO Clinical Stage. In multivariate analysis, longer duration on ART was a protective factor for viral non-suppression (13-24 months vs. >24 months: aOR = 8.92, 95% CI 2.60-30.61), while being on third line regimen (vs. first line) was protective against viral non-suppression (aOR = 0.11, 95% CI 0.03-0.49). A significant treatment gap is evident for ALHIV with high viral non-suppression levels. Interventions are required to counter treatment fatigue to keep adolescents engaged in ART, and timely switching to rescue regimens for failing adolescents.
Pyramid Fully Convolutional Network for Hyperspectral and Multispectral Image Fusion

Low spatial resolution hyperspectral (LRHS) and high spatial resolution multispectral (HRMS) image fusion has been recognized as an important technology for enhancing the spatial resolution of LRHS image. Recent advances in convolutional neural network have improved the performance of state-of-the-art fusion methods. However, it is still a challenging problem to effectively explore the spatial information of HRMS image. In this paper, we propose a pyramid fully convolutional network made up of an encoder sub-network and a pyramid fusion sub-network to address this issue. Specifically, the encoder sub-network aims to encode the LRHS image into a latent image. Then, this latent image, together with a HRMS image pyramid input, is used to progressively reconstruct the high spatial resolution hyperspectral image in a global-to-local manner. Furthermore, to sharpen the blurry predictions easily obtained by the standard l(2) loss, we introduce the gradient difference loss as a regularization term. We evaluate the proposed method on three datasets acquired by three different satellite sensors. Experimental results demonstrate that the proposed method achieves better performance than several state-of-the-art methods.
Advancing a causal role of type 2 diabetes and its components in developing macro- and microvascular complications via genetic studies

The role of diabetes in developing microvascular and macrovascular complications has been subject to extensive research. Despite multiple observational and genetic studies, the causal inference of diabetes (and associated risk factors) on those complications remains incomplete. In this review, we focused on type 2 diabetes, as the major form of diabetes, and investigated the evidence of causality provided by observational and genetic studies. We found that genetic studies based on Mendelian randomization provided consistent evidence of causal inference of type 2 diabetes on macrovascular complications; however, the evidence for causal inference on microvascular complications has been somewhat limited. We also noted high BMI could be causal for several diabetes complications, notable given high BMI is commonly upstream of type 2 diabetes and the recent calls to target weight loss more aggressively. We emphasize the need for further studies to identify type 2 diabetes components that mostly drive the risk of those complications. Even so, the genetic evidence summarized broadly concurs with the need for a multifactorial risk reduction approach in type 2 diabetes, including addressing excess adiposity.
Eye drop delivery of pigment epithelium-derived factor-34 promotes retinal ganglion cell neuroprotection and axon regeneration

Axotomised retinal ganglion cells (RGCs) die rapidly by apoptosis and fail to regenerate because of the limited availability of neurotrophic factors and a lack of axogenic stimuli. However, we have recently showed that pigment epithelium-derived factor (PEDF) promotes RGC survival and axon regeneration after optic nerve crush injury. PEDF has multiple fragments of the native peptide that are neuroprotective, anti-angiogenic and anti-inflammatory. Here we investigated the neuroprotective and axogenic properties of a fragment of PEDF, PEDF-34, in retinal neurons in vitro and when delivered by intravitreal injection and eye drops in vivo. We found that PEDF-34 was 43% more neuroprotective and 52% more neuritogenic than PEDF-44 in vitro. Moreover, in vivo, intravitreal delivery of 1.88nM PEDF-34 was 71% RGC neuroprotective at 21days after optic nerve crush compared to intact controls, whilst daily eye drops containing 1.88nM PEDF-34 promoted 87% RGC survival. After topical eye drop delivery, PEDF-34 was detected in the vitreous body within 30min and attained physiologically relevant concentrations in the retina by 4h peaking at 1.4±0.05nM by 14days. In eye drop- compared to intravitreal-treated PEDF-34 animals, 55% more RGC axons regenerated 250μm beyond the optic nerve lesion. We conclude that daily topical eye drop application of PEDF-34 is superior to weekly intravitreal injections in promoting RGC survival and axon regeneration through both direct effects on retinal neurons and indirect effects on other retinal cells.
Robust CP Tensor Factorization With Skew Noise

The low-rank tensor factorization (LRTF) technique has received increasing popularity in data science, especially in computer vision applications. Many robust LRTF models have been presented recently. However, none of them take the skewness of data into account. This letter proposes a novel LRTF model for skew data analysis by modeling noise as a Mixture of Asymmetric Laplacians (MoAL). The numerical experiments show that the new model MoAL-LRTF outperforms several state-of-the-art counterparts. The codes for all the experiments are available at https://xsxjtu.github.io/Projects/MoAL/main.html.