Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction and Identification of Krüppel-Like Transcription Factors by Machine Learning Method.

AIM AND OBJECTIVE The Krüppel-like factors (KLFs) are a family of containing Zn finger(ZF) motif transcription factors with 18 members in human genome, among them, KLF18 is predicted by bioinformatics. KLFs possess various physiological function involving in a number of cancers and other diseases. Here we perform a binary-class classification of KLFs and non-KLFs by machine learning methods. MATERIAL AND METHOD The protein sequences of KLFs and non-KLFs were searched from UniProt and randomly separate them into training dataset(containing positive and negative sequences) and test dataset(containing only negative sequences), after extracting the 188-dimensional(188D) feature vectors we carry out category with four classifiers(GBDT, libSVM, RF, and k-NN). On the human KLFs, we further dig into the evolutionary relationship and motif distribution, and finally we analyze the conserved amino acid residue of three zinc fingers. RESULTS The classifier model from training dataset were well constructed, and the highest specificity(Sp) was 99.83% from a library for support vector machine(libSVM) and all the correctly classified rates were over 70% for 10-fold cross-validation on test dataset. The 18 human KLFs can be further divided into 7 groups and the zinc finger domains were located at the carboxyl terminus, and many conserved amino acid residues including Cysteine and Histidine, and the span and interval between them were consistent in the three ZF domains. CONCLUSION Two classification models for KLFs prediction have been built by novel machine learning methods.
The Epidemiology of Alcohol-Induced Pancreatitis

Although the association between alcohol and pancreatitis has been recognized for centuries, the precise magnitude of the impact of alcohol remains poorly quantified. Epidemiologic research on this condition has been seriously handicapped by several factors. Classifications are based on morphology rather than on etiology; the diagnostic differences between acute and chronic pancreatitis are imprecise and confusing; and coding by the International Classification of Diseases (ICD) has been inadequate. The current ICD (ICD-10), used in the United States since 1999, identifies alcohol-induced chronic pancreatitis as a separate code for the first time, an enhancement that will greatly improve the quality of data collected in current and future studies. Unfortunately, no code yet exists for acute alcoholic pancreatitis. Of the approximately 2.4 million deaths in the United States in 1999, pancreatitis was listed as the underlying cause for 3289 deaths, making it the 235th leading cause of death. Acute pancreatitis accounted for 84% of these deaths, and chronic pancreatitis the remaining 16%. Alcohol is a primary cause of both acute and chronic pancreatitis in most developed countries. About one-third of acute pancreatitis in the United States is alcohol-induced. In the United States and other developed countries, 60%–90% of chronic pancreatitis is alcohol induced. Both forms are more common in men. The development of chronic pancreatitis is proportional to the dose and duration of alcohol consumption (minimum, 6–12 years of approximately 80g of alcohol per day). Autopsy studies reveal subclinical chronic pancreatitis in another 10% of alcohol abusers. Yet, since <10% of chronic alcoholics develop chronic pancreatitis, clearly other predisposing factors besides alcohol are involved. Genetic variability and environmental exposures, such as diet, are prime candidates for further investigation. To date, there have been few large epidemiological studies of alcoholic pancreatitis in the United States or other developed countries. Additional studies are needed to improve the quality of existing baseline epidemiologic data and allow better assessment of risk. Improved diagnostic precision, more complete and specific coding, and greater understanding of covariables and mechanisms would also advance the field.
Latency-Associated Nuclear Antigen (LANA) of Kaposi's Sarcoma-Associated Herpesvirus Interacts with Origin Recognition Complexes at the LANA Binding Sequence within the Terminal Repeats

ABSTRACT Kaposi's sarcoma-associated herpesvirus (KSHV) DNA persists in latently infected cells as an episome via tethering to the host chromosomes. The latency-associated nuclear antigen (LANA) of KSHV binds to the cis-acting elements in the terminal repeat (TR) region of the genome through its carboxy terminus. Previous studies have demonstrated that LANA is important for episome maintenance and replication of the TR-containing plasmids. Here we report that LANA associates with origin recognition complexes (ORCs) when bound to its 17-bp LANA binding cognate sequence (LBS). Chromatin immunoprecipitation of multiple regions across the entire genome from two KSHV-infected cell lines, BC-3 and BCBL-1, revealed that the ORCs predominantly associated with the chromatin structure at the TR as well as two regions within the long unique region of the genome. Coimmunoprecipitation of ORCs with LANA-specific antibodies shows that ORCs can bind and form complexes with LANA in cells. This association was further supported by in vitro binding studies which showed that ORCs associate with LANA predominantly through the carboxy-terminal DNA binding region. KSHV-positive BC-3 and BCBL-1 cells arrested in G1/S phase showed colocalization of LANA with ORCs. Furthermore, replication of The TR-containing plasmid required both the N- and C termini of LANA in 293 and DG75 cells. Interestingly, our studies did not detect cellular ORCs associated with packaged viral DNA as an analysis of purified virions did not reveal the presence of ORCs, minichromosome maintenance proteins, or LANA.
Ferromagnetism in the two-dimensional periodic Anderson model

Using the constrained-path Monte Carlo method, we studied the magnetic properties of the two-dimensional periodic Anderson model for electron fillings between $1/4$ and $1/2. $ We also derived two effective low-energy theories to assist in interpreting the numerical results. For $1/4$ filling, we found that the system can be a Mott or a charge-transfer insulator, depending on the relative values of the Coulomb interaction and the charge-transfer gap between the two noninteracting bands. The insulator may be a paramagnet or antiferromagnet. We concentrated on the effect of electron doping on these insulating phases. Upon doping we obtained a partially saturated ferromagnetic phase for low concentrations of conduction electrons. If the system were a charge-transfer insulator, we would find that the ferromagnetism is induced by the well-known Ruderman-Kittel-Kasuya-Yosida interaction. However, we found a novel correlated hopping mechanism inducing the ferromagnetism in the region where the nondoped system is a Mott insulator. Our regions of ferromagnetism spanned a much smaller doping range than suggested by recent slave boson and dynamical mean-field theory calculations, but they were consistent with that obtained by density-matrix renormalization group calculations of the one-dimensional periodic Anderson model.
Optimisation énergétique de data centers par utilisation de liquides pour le refroidissement des baies informatiques

Les data centers sont des infrastructures qui hebergent un grand nombre d’equipements informatiques. Plus de 99% de la puissance electrique consommee par les composants electroniques est transformee en chaleur. Pour assurer leur bon fonctionnement il est donc necessaire de les refroidir. Cette operation est majoritairement realisee par l’emploi de systemes de climatisation a air tres energivores. De plus, la densite de puissance dissipee au sein des baies informatiques est en augmentation permanente. Nous arrivons alors aux limites de l’utilisation de l’air comme fluide caloporteur pour le refroidissement. Les etudes realisees durant cette these concernent l’amelioration de l’efficacite energetique des systemes de refroidissement des baies electroniques par l’exploitation de liquides comme fluides caloporteurs. Cette approche permet de beneficier de coefficients d’echanges thermiques et de capacites de refroidissement plus importants, avec des perspectives plus viables pour la revalorisation de la chaleur issue des data centers.Durant la these, quatre solutions de refroidissement ont ete evaluees. Des experimentations ont ete menees a l’echelle de serveurs et d’une baie informatique. Une instrumentation consequente permet de mettre en evidence le bon refroidissement des composants et de determiner des indicateurs d’efficacite energetique des systemes etudies. A partir des resultats experimentaux, deux modeles numeriques sont developpes par une approche nodale et une identification des parametres par methode inverse. Ces modeles pourront etre dupliques a l’echelle d’une salle informatique afin de quantifier les gains potentiels de deux solutions de refroidissement liquide.
Probabilistic approach for maximum likelihood estimation of pose using lines

In this study, the authors have proposed a new solution for the problem of pose estimation from a set of matched 3D model and 2D image lines. Traditional line-based pose estimation methods utilising the finite information of the observations are based on the assumption that the noises for the two endpoints of the image line segment are statistically independent. However, in this study, the authors prove that these two noises are negatively correlative when the image line segment is fitted by the least-squares technique from the noisy edge points. Moreover, the authors derive the noise model describing the probabilistic relationship between the 3D model line and their finite image observations. Based on the proposed noise model, the maximum-likelihood approach is exploited to estimate the pose parameters. The authors have carried out synthetic experiments to compare the proposed method to other pose optimisation methods in the literature. The experimental results show that the proposed methods yield a clear higher precision than the traditional methods. The authors also use real image sequences to demonstrate the performance of the proposed method.
A Social Network Analysis based approach to deriving knowledge about research scenarios in a set of countries

In this paper, we propose a new Social Network Analysis based approach to providing a multi-dimensional picture of the research scenarios of a set of countries of interest and to detecting possible hubs operating therein. This knowledge allows the understanding of the impact of diﬀerent socio-economic conditions on research. Furthermore, it may support the design of policies for sustaining the accumulation of scientiﬁc and technological capabilities. We apply our approach to four North African countries (i.e., Algeria, Egypt, Morocco and Tunisia) in such a way as to show its potential.
The Self and Autobiographical Memory: Correspondence and Coherence

Abstract A modified version of Conway and Pleydell-Pearce's Self Memory System (SMS) account of autobiographical memory and the self is introduced. Modifications include discussion of a fundamental tension between adaptive correspondence (experience-near sensory-perceptual records of goal activity) and self-coherence (a more abstracted and conceptually-rich long-term store of conceptual and remembered knowledge). This tension is examined in relation to each SMS component—the episodic memory system, long-term self, and the working self. The long-term self, a new aspect of the model, consists of the interaction of the autobiographical knowledge base and the conceptual self. The working self, depending on goal activity status, mediates between episodic memory and the long-term self. Applications of the SMS to personality and clinical psychology are provided through analysis of self-defining memories and adult attachment categories, as well as case histories of traumatic memory. The SMS's role in imagination .
Materials characterization of explanted polypropylene hernia mesh: Patient factor correlation

This study quantitatively assessed polypropylene (PP) hernia mesh degradation and its correlation with patient factors including body mass index, tobacco use, and diabetes status with the goal of improving hernia repair outcomes through patient-matched mesh. Thirty PP hernia mesh explants were subjected to a tissue removal process followed by assessment of their in vivo degradation using Fourier transform infrared, differential scanning calorimetry, and thermogravimetric analysis analyses. Results were then analyzed with respect to patient factors (body mass index, tobacco use, and diabetes status) to determine their influence on in vivo hernia mesh oxidation and degradation. Twenty of the explants show significant surface oxidation. Tobacco use exhibits a positive correlation with modulated differential scanning calorimetry melt temperature and exhibits significantly lower TGA decomposition temperatures than non-/past users. Chemical and thermal characterization of the explanted meshes indicate measurable degradation while in vivo regardless of the patient population; however, tobacco use is correlated with less oxidation and degradation of the polymeric mesh possibly due to a reduced inflammatory response.
A risk for hepatocellular carcinoma persists long-term after sustained virologic response in patients with hepatitis C-associated liver cirrhosis.

BACKGROUND The long-term effect of sustained virologic response (SVR) to antiviral therapy on the risk of developing hepatocellular carcinoma (HCC), liver complications, liver-related death, and overall death in hepatitis C virus (HCV)-infected patients with liver cirrhosis is not fully known. METHODS These risks were evaluated during long-term follow-up in 351 patients with HCV-related cirrhosis. One hundred ten patients with SVR, 193 with non-SVR, and 48 who were untreated were included in a multicenter cohort that was initiated in 2001 and prospectively followed up for a mean of 5.3 (SD, 2.8) years. Complementary follow-up data from national registries were used to minimize the loss of patients during follow-up. RESULTS Six patients with SVR developed HCC at 0.04, 0.64, 2.4, 7.4, 7.4, and 7.6 years, respectively, after achieving SVR. The incidences of HCC, any liver complication, liver-related death, and overall death per 100 person-years were significantly lower in SVR time with 1.0, 0.9, 0.7, and 1.9, compared to 2.3, 3.2, 3.0, and 4.1 in non-SVR and 4.0, 4.9, 4.5, and 5.1 in untreated time. The long-term consequences did not decline significantly after >3 years versus during the first 3 years of follow-up. CONCLUSIONS The risk for HCC, liver decompensation, and death in patients with liver cirrhosis related to HCV was markedly reduced after SVR, but a long-term risk of developing HCC remains for up to 8 years. Cirrhotic patients with HCV who achieve SVR should therefore maintain long-term surveillance for HCC. Future studies aimed to better identify those with remaining long-term risk for HCC are needed.
Automatically prevention of accidentally maintenance system

World became a place where the human is not the principal generator of working force. In nowadays engineers created almost all industries fully automated, where the people are only supervising the production. All this industry that is highly automated had become dependent for the spare parts and maintenance. When it's appearing a problem in a highly automated industry it may be possible a halt in production. The best solutions for the accidental maintenance preventions are expensive and it is necessary to stop the production, and it isn't known the usage or the problems of the parts that are changed. The system proposed to use all parts that are mounted on the machine at the highest yield. Our system will make a monitoring for all components on the machines and it will alarm maintenance team if one component can have a failure until next stop of the machine. In this paper, you can find all the information that can sustain the idea of automatically accidentally prevention system to be used in the industry.
Managed Care as a Vehicle for Delivering More Effective Chronic Care for Older Persons

Chronic illness is now the dominant feature of health care, and its impact will grow with the aging of the population. Managed care could provide an environment conducive to better care for chronically ill patients. A precondition for these activities is a shift in Medicare payment approaches to managed care organizations to recognize differences in risk. To improve care for the chronically ill, changes need to occur in two major areas: (1) The approach to chronic care needs to become more aggressive, with higher expectations about the benefits from care (even if measured by slowing the rate of decline), and (2) an information infrastructure is needed to help focus clinicians' attention on changes in patients' status. Some of these changes may eventually evolve spontaneously in managed care's search for more efficient ways of meeting its service obligations, but external forces, such as certification and federal mandates, could catalyze the transition. J Am Geriatr Soc 46:1034–1039, 1998.
What is the Relationship About? - Extracting Information about Relationships from Wikipedia

What is the relationship between terms? Document analysis tells us that ”Crime” is close to ”Victim” and not so close to ”Banana”. While for common terms like Sun and Light the nature of the relationship is clear, the measure becomes more fuzzy when dealing with more uncommonly used terms and concepts and partial information. Semantic relatedness is typically calculated from an encyclopedia like Wikipedia, but Wikipedia contains a lot of information that is not common knowledge. So, when a computer calculates that Belarus and Ukraine are closely related, what does it mean to me as a human? In this paper, we take a look at perceived relationship and qualify it in a human-readable way. The result is a search engine, designed to take two terms and explain how they relate to each other. We evaluate this through a user study which gauges how useful this extra information is to humans when making a judgment about relationships.
Patología molecular y diagnóstico de enformedades infecciosas

Los autores revisan y describe metodos moleculares para la deteccion de agentes etiologicos o secuencias geneticas involucradas en la patogenesis de varias enfermedades. Hay sondas moleculares ya disponibles para el diagnostico rapido de enfermedades causadas por un gran numero de virus, bacterias, hongos, espiroquetas, rickettsias y otros agentes infecciosos. Dado que las sondas de acidos nucleicos pueden distinguir muy pequenas diferencias indicativas de mutaciones geneticas o alteraciones, se pueden desarrollar sondas especificas aun para aquellas enfermedades con agentes etiologicos desconocidos. Ademas usando estas tecnicas se han identificado cepas resistentes a medicamentos y cepas patogenas asociadas a epidemias en areas ampliamente separadas de un pais o de una ciudad. Asi pues la sensibilidad y la especificidad de los metodods de deteccion molecular usando sondas radioactivas y no radioactivas estan a tal punto que se pueden aplicar a especimenes clinicos para el diagnostico rapido e identificacion de agentes etiologicos responsables de la patogenia de una variedad de enfermedades
Primary cutaneous leiomyosarcoma: clinicopathological analysis of 36 cases

Massi D, Franchi A, Alos L, Cook M, Di Palma S, Enguita A B, Ferrara G, Kazakov D V, Mentzel T, Michal M, Panelos J, Rodriguez‐Peralto J L, Santucci M, Tragni G, Zioga A & Tos A P D (2010) Histopathology56, 251–262
Streptozocin-Based Chemotherapy in Patients with Advanced Neuroendocrine Neoplasms – Predictive and Prognostic Markers for Treatment Stratification

Background and Aim Chemotherapy with streptozocin (STZ) in combination with 5-FU or doxorubicin (Dox) represents a standard of care for patients with metastatic pancreatic neuroendocrine neoplasms (pNEN). However, predictive markers for patient selection are still missing. The aim of this study was a retrospective evaluation of the clinicopathological characteristics of pNEN patients receiving STZ-based chemotherapies and to identify predictive and prognostic markers. Patients and Methods We retrospectively analyzed 77 patients treated at our center between 1995 and 2013. The median overall survival (OS) and progression-free survival (PFS) were calculated using Kaplan-Meier and Cox regression methods, respectively. Uni- and multivariate analyses were performed. Results The median PFS (mPFS) in patients receiving STZ/5-FU/Dox was 16 months with a median OS (mOS) of 28 months. Objective response rate (ORR) and disease control rate (DCR) were 34% and 72%, respectively. Biochemical response and positive octreotide scintigraphy predicted objective response. Univariate analysis revealed Ki-67 > 10% and the absence of biochemical or objective response by imaging as independent risk factors for shorter PFS. Additionally, performance status (PS) and resection of the primary tumor were observed to influence mOS. Treatment was well tolerated with less than 10% grade 3 and 4 toxicities. Conclusions STZ-based chemotherapy is an effective and well-tolerated treatment option in patients with well differentiated neuroendocrine neoplasms. Positive octreotide scintigraphy and biochemical response predict objective response.
Sensitivity of Gate-All-Around Nanowire MOSFETs to Process Variations—A Comparison With Multigate MOSFETs

This paper investigates the sensitivity of gate-all-around (GAA) nanowire (NW) to process variations compared with multigate devices using analytical solutions of Poisson's equation verified with device simulation. GAA NW and multigate devices with both heavily doped and lightly doped channels have been examined regarding their immunity to process-induced variations and dopant number fluctuation. Our study indicates that the lightly doped GAA NW has the smallest threshold voltage (V th) dispersion caused by process variations and dopant number fluctuation. Specifically, the GAA NW shows better immunity to channel thickness variation than multigate devices because of its inherently superior surrounding gate structure. For heavily doped devices, dopant number fluctuation may become the dominant factor in the determination of overall V th variation. The V th dispersion of GAA NW may therefore be larger than that of multigate MOSFETs because of its larger surface-to-volume ratio.
A Fast GPU Based High-Quality Three-Dimensional Visualization Method

Three-dimensional visualization is one of the most important researches in the field of medical images processing. Volume rendering is a powerful technique for visualizing meaningful information extracted from volumetric data in three-dimensional visualization. Although it does not need to generate intermediate geometric primitives and its rendering result is high quality, computational complexity of volume rendering is too high to achieve real-time interaction. Therefore, a fast GPU based high-quality three-dimensional visualization volume rendering method is proposed. A GPU based method is proposed to improve the run-time efficiency of volume rendering using volumetric texture. Because of limitation of video memory storage, large-scale volumetric data cannot be reconstructed or an expensive GPU is required. Therefore a slice texture based volume rendering method is proposed, which merely cost 4MB video memory by making use of a real-time dynamic switch mechanism. On the other hand, in order to eliminate annular distortion of volume rendering, a GPU based pre-integration classification method is presented. Although our methods are all implemented at general PCs, they can not only guarantee image quality but also improve rendering speed.