Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetics of Female Infertility: Molecular Study of Newborn Ovary Homeobox Gene in Poor Ovarian Responders

Background: Newborn ovary homeobox (NOBOX) gene plays a critical role in the transcriptional regulation of oocyte-specific genes. Previous studies have demonstrated a pathogenic effect of NOBOX variants on premature ovarian insufficiency (POI) patients. Poor ovarian response (POR) is a risk factor for POI. Therefore, genetic variants in the NOBOX gene may also be studied as risk factors for POR development. Aims: The aim of the study is to investigate the association between seven known NOBOX single-nucleotide polymorphisms (SNPs) and POR in Jordanian females. Settings and Design: This was a case–control study of 60 females with POR for controlled ovarian hyperstimulation and 59 healthy females with no history of reproductive problems. Blood samples were collected from the participants and seven SNPs of NOBOX gene were screened. Subjects and Methods: DNA was extracted from blood samples. Polymerase chain reaction with primers specific for seven known SNPs in NOBOX gene was used to amplify the specified region within the gene followed by Sanger sequencing. Results: The seven SNPs investigated in this study, namely, rs77587352 (c.271G>T, p. Gly91Trp), rs7800847 (c.349C>T, p. Arg117Trp), rs193303102 (c.907C>T, p. Arg303X), rs193303103 (c.1025G>C, p. Ser342Thr), rs193303104 (c.1048G>T, p. Val350Leu), rs201947677 (c.1064G>A, p. Arg355His), and rs146227301 (c.1856C>T, p. Pro619Leu), only represent the wild-type allele in both females with POR and healthy participants. Conclusions: The results show that only monomorphic genotype of the NOBOX variants was found in Jordanian females studied.
Disease Management plus Recommended Care versus Recommended Care Alone for Ambulatory Patients with Chronic Obstructive Pulmonary Disease

Rationale: The efficacy of disease management programs in the treatment of patients with chronic obstructive pulmonary disease (COPD) remains uncertain. Objectives: To study the effect of disease management (DM) added to recommended care (RC) in ambulatory patients with COPD. Measurements and Main Results: In this trial, 1,202 patients with COPD (age, ≥40 yr), with moderate to very severe airflow limitation were randomly assigned either to DM plus RC (study intervention) or to RC alone (control intervention). RC included follow‐up by pulmonologists, inhaled long‐acting bronchodilators and corticosteroids, smoking cessation intervention, nutritional advice and psychosocial support when indicated, and supervised physical activity sessions. DM, delivered by trained nurses during patients' visits to the designated COPD centers and by remote contacts with the patients between these visits, included patient self‐care education, monitoring patients' symptoms and adherence to treatment, provision of advice in case of acute disease exacerbation, and coordination of care vis‐à‐vis other healthcare providers. The primary composite endpoint was first hospital admission for respiratory symptoms or death from any cause. During 3,537 patient‐years, 284 patients (47.2%) in the control group and 264 (44.0%) in the study intervention group had a primary endpoint event. The median (range) time elapsed until a primary endpoint event was 1.0 (0‐4.0) years among patients assigned to the study intervention and 1.1 (0‐4.1) years among patients assigned to the control intervention; adjusted hazard ratio, 0.92 (95% confidence interval, 0.77‐1.08). Conclusions: DM added to RC was not superior to RC alone in delaying first hospital admission or death among ambulatory patients with COPD.
Kidney Tumors Associated With Hereditary Cancer Syndromes: An Emerging Opportunity and Responsibility in Surgical Pathology

Abstract Recent years have seen a proliferation of new entities in renal neoplasia, especially renal cell carcinoma. In particular, several of these entities frequently present as part of hereditary cancer predisposition syndromes and have been variably classified based on associated syndromal names and features, eponyms, or based on the causative genetic or biochemical defect. Overall, we would argue that assisting in recognition of any hereditary cancer predisposition, however aggressive or however penetrant, is an opportunity for distinct and growing added value in contemporary pathology. In several cases, the kidney tumors or their associated syndromal stigmata are aggressive or may trigger ongoing surveillance or specific interventions for affected patients and family members. Prior experience with these tumors has led us to realize that we are frequently evaluating specimens with limited clinical context, let alone sufficient family history. The most subtle clues, whether from the gross room, the histomorphology, the laboratory information system, or the medical record, have proven essential in the recognition of these tumors. Highlighting close clinicopathologic correlation, as well as collaboration between subspecialty areas in surgical pathology, these contextual clues to several syndromal kidney tumors form the basis of a growing opportunity and responsibility in surgical pathology.
Characterization of Molecular Alterations in an Unusual Case of Lynch Syndrome–Associated Adrenocortical Carcinoma

Abstract The criteria for diagnosing both Lynch syndrome and adrenocortical carcinoma have been well established in previous literature. However, diagnostic challenges still arise in distinguishing adrenocortical adenoma from adrenocortical carcinoma, as well as in screening patients for neoplasms that are potentially associated with Lynch syndrome. We present a case of Lynch syndrome–associated adrenocortical carcinoma in a patient carrying a germline MSH2 mutation. Although Lynch syndrome–associated adrenocortical carcinoma is a well-documented entity, this particular tumor demonstrated an unusual immunohistochemical staining pattern for DNA mismatch repair proteins, as well as a complicated histopathologic pattern. Via molecular testing, the biologic nature of the tumor was confirmed. This case study provides clarification on both appropriate Lynch syndrome screening testing procedures and molecular results, which would help confirm malignant potential in adrenal cortical neoplasms.
Burden of caregiving and its impact in the patients of acute lymphoblastic leukemia

Aim: This study aims to study the caregiver burden and its correlates among the caregivers of adolescent and adult patients of acute lymphoblastic leukemia (ALL). Materials and Methods: Sixty caregivers of patients with ALL were assessed on Family Burden Interview Schedule (FBI), Caregiver Strain Index, multidimensional aspect of perceived social support scale, Cognitive–Behavioral Avoidance Scale, ways of coping checklist, and General Health Questionnaire. Results: Caregivers of patients with ALL reported high caregiver burden (FBI objective burden score – 21.77; subjective burden score – 1.83). Among the domains of FBI, the highest burden was seen in the form of financial burden closely followed by disruption of family leisure. Caregivers of male patients and those belonging to higher socioeconomic status reported higher level of objective burden. Caregiver burden was higher among caregivers who reported lower perceived social support, who more often used avoidance and escape as coping and less often used planful problem solving. Higher caregiver burden is associated with higher psychological morbidity. Conclusion: Caregivers of patients with ALL experience high level of caregiver burden and it is associated with lower social support and more often use maladaptive coping strategies.
Image and figure quality

Abstract After purchasing Elsevier's Earth and Planetary Sciences electronic journal back file package, problems with image and figure quality in articles became evident. Personnel at Elsevier verbally committed to rescanning any issues having at least one image or figure of unacceptable quality, if staff at University of Illinois at Urbana-Champaign would identify the problem issues. A study of 35 titles in the Earth and Planetary Sciences back file package revealed that, of the 6038 issues published before digital format was available, 73.6% had at least one image with unacceptable quality. The implications of poor image quality in electronic journals should be considered when libraries are deciding whether to discard print copies. Publishers and librarians should work together to ensure that print journals converted to digital format are of acceptable quality.
Six‐Month Outcome of Immunocompromised Patients with Severe Acute Respiratory Distress Syndrome Rescued by Extracorporeal Membrane Oxygenation. An International Multicenter Retrospective Study

Rationale: Because encouraging rates for hospital and long‐term survival of immunocompromised patients in ICUs have been described, these patients are more likely to receive invasive therapies, like extracorporeal membrane oxygenation (ECMO). Objectives: To report outcomes of immunocompromised patients treated with ECMO for severe acute respiratory distress syndrome (ARDS) and to identify their pre‐ECMO predictors of 6‐month mortality and main ECMO‐related complications. Methods: Retrospective multicenter study in 10 international ICUs with high volumes of ECMO cases. Immunocompromised patients, defined as having hematological malignancies, active solid tumor, solid‐organ transplant, acquired immunodeficiency syndrome, or long‐term or high‐dose corticosteroid or immunosuppressant use, and severe ECMO‐treated ARDS, from 2008 to 2015 were included. Measurements and Main Results: We collected demographics, clinical data, ECMO‐related complications, and ICU‐ and 6 month‐outcome data for 203 patients (median Acute Physiology and Chronic Health Evaluation II score, 28 [25th‐75th percentile, 20‐33]; age, 51 [38‐59] yr; PaO2/FiO2, 60 [50‐82] mm Hg before ECMO) who fulfilled our inclusion criteria. Six‐month survival was only 30%, with a respective median ECMO duration and ICU stay of 8 (5‐14) and 25 (16‐50) days. Patients with hematological malignancies had significantly poorer outcomes than others (log‐rank P = 0.02). ECMO‐related major bleeding, cannula infection, and ventilator‐associated pneumonia were frequent (36%, 10%, and 50%, respectively). Multivariate analyses retained fewer than 30 days between immunodeficiency diagnosis and ECMO cannulation as being associated with lower 6‐month mortality (odds ratio, 0.32 [95% confidence interval, 0.16‐0.66]; P = 0.002), and lower platelet count, higher Pco2, age, and driving pressure as independent pre‐ECMO predictors of 6‐month mortality. Conclusions: Recently diagnosed immunodeficiency is associated with a much better prognosis in ECMO‐treated severe ARDS. However, low 6‐month survival of our large cohort of immunocompromised patients supports restricting ECMO to patients with realistic oncological/therapeutic prognoses, acceptable functional status, and few pre‐ECMO mortality‐risk factors.
Immediate Functional Loading: Results for the Concept of the Strategic Implant®

Background: Immediate functional loading of one-piece dental implants has become an accepted treatment modality for fixed restorations in fully edentulous mandibles and maxillae. Nevertheless, studies regarding immediate loading procedures in extraction sites in both the jaws, as well as in segment reconstructions and single-tooth replacements, are limited. Purpose: The purpose of this study was to evaluate the presently used protocol for immediate functional loading (within maximum 3 days) of one-piece implants which are placed according to the following methods as published by the IF. Materials and Methods: This prospective cohort study included totally 87 consecutively treated patients who receive 1169 immediately loaded one-piece Strategic Implant®, supporting fixed complete-arch maxillary or mandibular metal-ceramic bridges or segment reconstructions in both the jaws. All implants were placed by one treatment provider, who delivered also the prosthetics and controlled all cases himself over the years. Data were extracted by an experienced dentist from the patient records and from panoramic X-rays. A number of patients were interviewed at the end of the observation period. Although a total of 5100 implants were placed and observed for 12 – 57 months totally (with 105 implants out of these, having failed), this article reports the detailed results only for 1169 implants which have been followed for at least 48 months. Results: Immediate functional loading of using multiple, cortically anchored basal screw implants as a support for fixed full-arch and segment prosthesis in the upper and lower jaw demonstrated a high cumulative implant survival rate after an observation period of up to 57 months. Neither hypertension nor diabetes and neither smoking nor bending of the implant's neck had an influence on the success of the implants observed in this study. Within the limits of this study (5100 Strategic Implants were observed over a period of up to 57 months), “peri-implantitis” was not observed at all. Conclusion: The treatment concept developed for the technology of the Strategic Implant® is safe and effective and it avoids bone augmentations and “peri-implantitis”.
frailtypack: An R Package for the Analysis of Correlated Survival Data with Frailty Models Using Penalized Likelihood Estimation or Parametrical Estimation

Frailty models are very useful for analysing correlated survival data, when observations are clustered into groups or for recurrent events. The aim of this article is to present the new version of an R package called frailtypack. This package allows to fit Cox models and four types of frailty models (shared, nested, joint, additive) that could be useful for several issues within biomedical research. It is well adapted to the analysis of recurrent events such as cancer relapses and/or terminal events (death or lost to follow-up). The approach uses maximum penalized likelihood estimation. Right-censored or left-truncated data are considered. It also allows stratification and time-dependent covariates during analysis.
Proposals for classification methods dedicated to biological data

The number of available genomic sequences is growing very fast, due to the development of massive sequencing techniques. Sequence classification is needed and contributes to the assessment of gene and species evolutionary relationships. Classification methods are thus necessary to carry out these identification operations in an accurate and fast way. We develop a classification method dedicated to homologous sequence family databases, allowing the attribution of a new sequence to a cluster using similarity measures. We used this classification method to implement two applications, Homologous Sequence Identification (HoSeqI) and MultiHoSeqI. Lately, we developed a chimera detection method and implemented an application, Chimeric Sequence Identification (ChiSeqI) to automate the processes of classification of specific biological data, the bacterial 16S ribosomal RNA sequences, and of detection of chimeric sequences.
Migration of batch log-processing job from Apache Hadoop Map-Reduce to Apache Spark in the public cloud

With the increasing adoption of cloud-based infrastructure the problem of efficient utilization of provisioned resources becomes more important, since even in a pay-as-you-go model computing resources are allocated and charged in a coarse grained way (e.g. the whole virtual machine per hour). This problem becomes major in the batch processing systems, where computational resources are organized into a cluster. Even small optimization of applications running on such systems can result in significant cost savings. In this thesis we evaluate one such application - JournalProcessor, which is a batch log-processing job that aggregates and indexes logs containing metrics data. JournalProcessor application itself built using Apache Hadoop MapReduce engine that runs on top of Apache Hadoop YARN cluster resource manager, which is deployed onto Amazon EC2 public cloud using Amazon Elastic Map Reduce (EMR). The research question of this thesis is the following - is it possible to migrate JournalProcessor from Apache Hadoop MapReduce data processing engine to more general data-stream oriented system - Apache Spark? Our hypothesis is that by migrating the application to Spark, the utilization of provisioned cluster resources will increase, and the running time of the job will decrease. Our contributions include: description of the application to generate the workload (JournalProcessor), generic methodology for migrating MapReduce applications to Spark and the detailed evaluation of metrics produced by a cluster.
Calculation of average and variance bus currents for reliability analysis of VLSI CMOS circuits

Techniques for calculating average and variance of currents in various branches of power and ground buses are presented. These current estimates can be used to estimate mean time to failure due to electromigration in sections of the buses and to redesign them, if necessary, so that the electromigration failures over the estimated lifespan of the chip are minimized. The validity of the approach rests on the assumption that the bus can be modeled as a linear resistive network. The sparsity of this network is exploited to speed up the calculation of averages and variances. It is necessary to formulate and LU factorize the node admittance matrix only once. <<ETX>>
An Experimental Study of an Integrated GPS/INS System for Shallow-Water AUV Navigation (SANS)

The Naval Postgraduate School's "Phoenix" AUV has thus far been operated only in a test pool environment. In preparation for open water testing, currently planned for mid-1996, a series of towfish experiments are being conducted in Monterey Bay to investigate the feasibility of integrated GPS/INS transit mode navigation, in significant sea states, using a GPS antenna mounted only a few inches above the AUV body. In this configuration, either wave action or deliberate submergence will cause loss of GPS position fix information for periods extending from several seconds to a few minutes. The main research question being investigated is, therefore, to determine whether or not a low cost strapped down IMU can be used to navigate accurately between GPS fixes. Our goal is to achieve inertial navigation accuracy comparable to GPS accuracy during periods between successive GPS fixes. Experimental results reported in this paper indicate that this is feasible.
lavaan: An R Package for Structural Equation Modeling

Structural equation modeling (SEM) is a vast field and widely used by many applied researchers in the social and behavioral sciences. Over the years, many software packages for structural equation modeling have been developed, both free and commercial. However, perhaps the best state-of-the-art software packages in this field are still closed-source and/or commercial. The R package lavaan has been developed to provide applied researchers, teachers, and statisticians, a free, fully open-source, but commercial-quality package for latent variable modeling. This paper explains the aims behind the development of the package, gives an overview of its most important features, and provides some examples to illustrate how lavaan works in practice.
High speed pipelined CMOS encoder for flash A/D converters

Different CMOS encoders for flash A/D (analog-to-digital) converters are compared from the speed and noise points of view. The proposed pipelined CMOS encoder gives a load capacitance to each comparator of no more than a unit inverter. The error probability of the encoder in the most significant bit is much less than that in the least significant bit. A true single-phase clock was used to achieve high speed and simple structure. A 6-bit flash A/D converter using very simple, nonlatched comparators associated with this encoder was fabricated in a 3- mu m CMOS process and tested. The highest sampling rate measured was 200 megasamples/s at a power supply of +or-3.5 V. <<ETX>>
Hopfield nets with time-varying energy functions for solving the travelling salesman problem

A novel method to solve the travelling salesman problem (TSP) with the Hopfield model is introduced. The method uses a time-varying energy function to enhance performance, instead of the simulated annealing approach of adding a random noise to the input of each neuron. The proposed energy function represents the TSP precisely and controls the process of convergence strictly. The method has obtained 100% optimal solutions within 300 iterations to the ten city problem with same map as that of J.J. Hopfield and D.W. Tank (1985), and has been proven very efficient for other sets of ten city problems whose cities are randomly and uniformly distributed within a unit square. Furthermore, some near-optimal solutions have also been found for larger-scale problems under the same circumstances. <<ETX>>
Simultaneous moving and uncovered-background pixel detection and parameter estimation in video sequences

Two essential aspects of uncovered-background prediction and motion compensation for image sequence coding are the segmentation of an image frame in a sequence of images into regions of uncovered- and covered-background, moving, and stationary pixels and the estimation of motion parameters. We have developed and investigated a method which simultaneously estimates motion and sequence parameters and provides image segmentation from noisy image sequences. The method segments an image frame in an image sequence into regions of moving, stationary, covered-background, and uncovered-background pixels relative to a reference frame. The basis of our method is the expectation-maximization algorithm for maximum-likelihood estimation. We previously presented our method under assumptions which imposed sever restrictions on the image composition and the object motion and did not consider covered-background pixels. These cases, though unrealistic, were illustrative of the mathematical formulation of our method. In this paper we remove the limiting restrictions on the image composition, and we introduce a region for covered-background pixels.