Miracle-dz/UniFAR-FTUs huggingface dataset:
What Motivates Occasional Faculty Developers to Lead Faculty Development Workshops? A Qualitative Study

Purpose The demand for faculty development is ongoing, and many medical schools will need to expand their pool of faculty developers to include physicians and scientists whose primary expertise is not education. Insight into what motivates occasional faculty developers can guide recruitment and retention strategies. This study was designed to understand the motivations of faculty developers who occasionally (one to three times each year) lead faculty development workshops. Method Qualitative data were collected in March and April 2012 from interviews with faculty developers who occasionally taught workshops from 2007 to 2012 in the University of California, San Francisco, School of Medicine’s faculty development program. The interviews were audiotaped and transcribed. The authors thematically analyzed the transcripts using a general inductive approach and developed codes sensitized by motivation theories. Results The authors interviewed 29/30 (97%) occasional faculty developers and identified five themes: mastery (desire to learn and develop professionally), relatedness (enjoyment of working with and learning from others), duty (sense of obligation to give back and be a good academic citizen), purpose (commitment to improving local teaching and ultimately patient care), and satisfaction (fun and enjoyment). Conclusions Four of the themes the authors found are well addressed in motivation theory literature: mastery, relatedness, duty, and purpose. Whereas these four are motivators for occasional faculty developers, it is the fifth theme—satisfaction—that the authors feel is foundational and links the others together. Armed with this understanding, individuals leading faculty development programs can develop strategies to recruit and retain occasional faculty developers.
Own and partner pain intensity in older couples: longitudinal effects on depressive symptoms

Abstract Chronic pain has been linked to depression among individuals and their partners. Yet, little is known about long-term mutual influences between pain intensity and depressive symptoms within couples as they age. Using a nationally representative U.S. sample of wives and husbands aged 50 and older (mean = 64.53, SD = 7.86), this study explored the links between own and partner pain intensity and depressive symptoms across an 8-year period. A total of 963 heterosexual married couples drawn from the Health and Retirement Study completed interviews biennially from 2006 to 2014. Dyadic growth curve models examined mutual associations within couples and controlled for sociodemographic characteristics, length of marriage, and marital quality, along with self-rated health, number of chronic health conditions, and functional disability. For wives and husbands, their own greater baseline pain intensity was significantly linked to their own higher levels of depressive symptoms. Unexpectedly, wives with greater baseline pain intensity reported decreases in their depressive symptoms over time. There were also partner effects such that husbands' greater pain intensity at baseline was associated with increases in wives' depressive symptoms over time. Findings highlight the importance of considering both individual and spousal associations between pain intensity and depressive symptoms in later life. Understanding how individual and couple processes unfold may yield critical insights for the development of intervention and prevention efforts to maintain mental health among older chronic pain patients and their spouses.
Differentiation of Naegleria fowleri from Acanthamoeba species by using monoclonal antibodies and flow cytometry

Monoclonal antibodies to Naegleria fowleri and Acanthamoeba polyphaga were analyzed by enzyme-linked immunosorbent assay, indirect immunofluorescence microscopy, and fluorescence flow cytometry to assess specificity and cross-reactivity with axenically cultured N. fowleri and Acanthamoeba spp. Four monoclonal antibodies to N. fowleri were specific for N. fowleri and had no reactivity to A. polyphaga. Similarly, four monoclonal antibodies to A. polyphaga did not react with N. fowleri. Two of the four monoclonal antibodies to A. polyphaga did not react with other Acanthamoeba spp. tested, while two of the antibodies demonstrated a high degree of cross-reactivity with a putative Acanthamoeba castellanii strain by immunofluorescence microscopy; this was confirmed by fluorescence flow cytometry for one of the antibodies. These monoclonal antibodies were used to identify Acanthamoeba trophozoites in infected brain sections of a patient who died of suspected Acanthamoeba-caused granulomatous amoebic encephalitis, demonstrating potential utility in the direct identification of N. fowleri and Acanthamoeba spp. in clinical specimens.
Teacher Attitudes toward Latin Instruction at the Elementary Level

The purpose of this study was to identify whether teacher attitudes toward Latin instruction at the elementary level were generally positive or negative. Participants were elementary Latin and English Language Art teachers who had experience with students receiving Latin instruction in elementary classrooms. Data were collected through interviews. The elementary teachers were questioned about their general experience of Latin and their observations of Latin’s effects on other content areas. Differences in opinions between Latin instructors and English Language Arts instructors were recorded. This study benefits educators who are interested in teaching Latin as a content area or integrating Latin into a subject in an elementary level classroom. Thesis Mentor: ________________________ Dr. Yasar Bodur Honors Director: _______________________
Stereoscopic image quality prediction

Three-dimensional (3D) imaging has attracted considerable attention recently due to its increasingly wide range of applications. Consequently, perceived quality is a great important issue to assess the performance of all 3D imaging applications. Perceived distortion and depth of any stereoscopic images are strongly dependent on the local features, such as edge, flat and texture. In this paper, we propose an noreference (NR) perceptual quality assessment for JPEG coded stereoscopic images based on segmented local features of artifacts and disparity. The local features information of stereoscopic pair images such as edge, flat and texture areas and also the blockiness and zero crossing rate within the block of the images are evaluated for artifacts and disparity in this method. The result on our subjective stereoscopic images database indicates that the model performs quite well over a wide rang of image content and distortion levels.
Gauss–Newton inspired preconditioned optimization in large deformation diffeomorphic metric mapping

In this work, we propose a novel preconditioned optimization method in the paradigm of Large Deformation Diffeomorphic Metric Mapping (LDDMM). The preconditioned update scheme is formulated for the non-stationary and the stationary parameterizations of diffeomorphisms, yielding three different LDDMM methods. The preconditioning matrices are inspired in the Hessian approximation used in Gauss–Newton method. The derivatives are computed using Frechet differentials. Thus, optimization is performed in a Sobolev space, in contrast to optimization in L2 commonly used in non-rigid registration literature. The proposed LDDMM methods have been evaluated and compared with their respective implementations of gradient descent optimization. Evaluation has been performed using real and simulated images from the Non-rigid Image Registration Evaluation Project (NIREP). The experiments conducted in this work reported that our preconditioned LDDMM methods achieved a performance similar or superior to well-established-in-literature gradient descent non-stationary LDDMM in the great majority of cases. Moreover, preconditioned optimization showed a substantial reduction in the execution time with an affordable increase of the memory usage per iteration. Additional experiments reported that optimization using Frechet differentials should be preferable to optimization using L2 differentials.
Voltage and Current Selector-Based Biasing Topology for Multiple Supply Voltage Circuits

In systems-on-chip there are multiple supply voltage (MSV) designs in which a module is powered by several supply rails. For example, these rails are at 40, 5, and 3.3 V. A safe biasing scheme is needed to ensure no tri-stated biasing conditions can exist, which can result in unintended activation of the power stages or output drivers leading to high currents. It is shown here a safe biasing scheme can be implemented under any power sequencing scheme in MSV designs by exploiting the voltage and current selector topologies. This circuit was implemented in a 40-V, 0.35- $ \mu {\mathrm m}$ , BiCMOS process on a four-channel airbag squib driver IC. The fabricated circuit’s quiescent current is less than 5 mA even if the on chip junction temperature is 175 °C and for various fault conditions that can occur in a multiple power supply domain.
A multi-state model for evolution of intensive care unit patients: prediction of nosocomial infections and deaths.

Nosocomial (hospital-acquired) infections are very frequent in intensive care units (ICU). The risk of death after severe infection is high, but the precise rate of death in ICU attributable to nosocomial infection is not known. The goal of this project was to build a statistical model to predict the occurrence of nosocomial infections in ICU and the outcome of the patients. We collected data on 676 consecutive patients admitted to an ICU for more than 24 hours between 1993 and 1996. The following data were collected for each patient: history; clinical examination at entry; subsequent infections; outcome. A multi-state heterogeneous semi-Markov model was determined and then validated; the initial data set was randomly split into two groups: two-thirds (450 patients) to build the model and one-third (226 patients) to validate it. The model defined five states: ICU admission; first simple infection; first complicated infection; death, and discharge from the ICU. Transitions between these states determined nine different events. The global model of patient histories can be divided into nine survival models, each corresponding to one of these events. The possible events from a given state were considered to be competing. Since many risk factors induced non-proportional hazard functions, piecewise exponential models were used to model event occurrence. The effect of continuous covariates on hazard functions has been described with a non-parametric method that enables non-linear relations to be shown. Among other things, the model allows patients' post-admission histories to be predicted from data available at ICU admission. The bootstrap estimator of the attributable risk of death due to simple or complicated nosocomial infections is 44.2 percent (95 percent CI 26.0-61.6 percent). We were also able to characterize the most highly exposed patients, those who comprise the high-risk group on whom prevention efforts must be focused.
Highly Uneven Distribution of Tenofovir-Selected Simian Immunodeficiency Virus in Different Anatomical Sites of Rhesus Macaques

ABSTRACT Antiviral tenofovir monotherapy was used to determine whether drug-selected simian immunodeficiency virus (SIV) variants replaced their wild-type progenitors at the same rate in different tissues of six rhesus macaques. The relative frequencies of drug-resistant and wild-type genotypes were measured longitudinally in blood and in 23 lymphoid and nonlymphoid tissues collected at necropsy. The mutant/wild-type genotype ratio was measured using a heteroduplex tracking assay targeting tenofovir-selected SIV reverse transcriptase codons. After the initiation of tenofovir treatment in animals with high steady-state viremia levels, resistant genotypes emerged in the plasma within 1 to 8 weeks and in five of six cases reached frequencies of nearly 100% within 4 to 25 weeks. The appearance of tenofovir-resistant genotypes in peripheral blood mononuclear cell (PBMC) DNA was generally delayed by 1 to 2 weeks and in one case was completely absent. Necropsies performed 8 to 55 weeks after the initiation of tenofovir treatment showed the frequency of resistant SIV genotypes to be generally higher in tissue RNA than DNA fractions. The frequency of drug-resistant genotypes varied widely between anatomical sites, including different lymph nodes of the same animal. Except for the epidydimis, the tissues with the lowest rates of proviral replacement by tenofovir-resistant genotypes differed between animals. The highly uneven distribution of tenofovir-resistant genotypes in different tissues seen shortly after the initiation of tenofovir monotherapy may reflect differences in local antiviral drug selection pressures and/or the stochastic effect of small effective populations of drug-resistant variants randomly seeding different anatomical sites early in therapy.
Dissecting Stop Transfer versus Conservative Sorting Pathways for Mitochondrial Inner Membrane Proteins in Vivo*

Background: There has been no in vivo assay to determine mitochondrial membrane protein sorting. Results: The Mgm1 fusion approach provides a versatile experimental tool for determining the mitochondrial sorting pathways in vivo. Conclusion: Sorting of mitochondrial inner membrane proteins carrying moderately hydrophobic transmembrane segments are modulated, depending on the cellular environment. Significance: Mitochondrial membrane protein sorting may be a dynamic process. Mitochondrial inner membrane proteins that carry an N-terminal presequence are sorted by one of two pathways: stop transfer or conservative sorting. However, the sorting pathway is known for only a small number of proteins, in part due to the lack of robust experimental tools with which to study. Here we present an approach that facilitates determination of inner membrane protein sorting pathways in vivo by fusing a mitochondrial inner membrane protein to the C-terminal part of Mgm1p containing the rhomboid cleavage region. We validated the Mgm1 fusion approach using a set of proteins for which the sorting pathway is known, and determined sorting pathways of inner membrane proteins for which the sorting mode was previously uncharacterized. For Sdh4p, a multispanning membrane protein, our results suggest that both conservative sorting and stop transfer mechanisms are required for insertion. Furthermore, the sorting process of Mgm1 fusion proteins was analyzed under different growth conditions and yeast mutant strains that were defective in the import motor or the m-AAA protease function. Our results show that the sorting of mitochondrial proteins carrying moderately hydrophobic transmembrane segments is sensitive to cellular conditions, implying that mitochondrial import and membrane sorting in the physiological environment may be dynamically tuned.
Manual evaluation of tissue microarrays in a high‐throughput research project: The contribution of Indian surgical pathology to the Human Protein Atlas (HPA) project

The Human Protein Atlas (HPA) program (www.proteinatlas.org) is an international program that has been set up to allow for a systematic exploration of the human proteome using antibody‐based proteomics. This is accomplished by combining high‐throughput generation of affinity‐purified (mono‐specific) antibodies with protein profiling in a multitude of tissues/cell types assembled in tissue microarrays. Twenty‐six surgical pathologists over a seven‐and‐half year period have annotated and curated approximately sixteen million tissue images derived from immunostaining of normal and cancer tissues by approximately 23 000 antibodies. Web‐based annotation software that allows for a basic and rapid evaluation of immunoreactivity in tissues has been utilized. Intensity, fraction of immunoreactive cells and subcellular localization were recorded for each given cell population. A text comment summarizing the characteristics for each antibody was added. The methods used and the challenges encountered for this exercise, the largest effort ever by a single group of surgical pathologists, are discussed. Manual annotation of digital images is an important tool that may be successfully utilized in high‐throughput research projects. This is the first time an Indian private pathology laboratory has been associated with cutting‐edge research internationally providing a classic example of developed and emerging nation collaboration.
Post-traumatic Symptomatology in Parents with Premature Infants: A Systematic Review of the Literature

The emotional distress resulting from the experience of giving birth to a preterm infant (gestational age , 37 weeks) and the subsequent neonatal unit hospitalisation may be a traumatic experience for parents. In the present systematic literature review, studies on parental posttraumatic symptomatology following birth of a premature infant were reviewed. A total of 5 studies were identified. All studies reviewed found that posttraumatic symptomatology is quite common in parents or primary caregivers of premature infants. However, methodological weaknesses of relevant studies (e.g. use of convenience samples, lack of pre – delivery assessments) make it difficult to draw consistent conclusions regarding prevalence of posttraumatic symptomatology in this population group or whether the experience of a premature birth could be responsible for the development of PTSD. Directions for future research are discussed.
Mycobacterium tuberculosis Rv2179c Protein Establishes a New Exoribonuclease Family with Broad Phylogenetic Distribution*

Background: More than 25% of Mtb proteins have unknown functions, limiting our understanding of Mtb physiology and pathogenesis. Results: The hypothetical Mtb protein Rv2179c is a new DEDD-type exoribonuclease. Conclusion: Rv2179c is the founding member of a new exoribonuclease family with broad phylogenetic distribution. Significance: Assigning RNase function to Rv2179c provides annotation for hundreds of bacterial orthologs and provides a new view of RNA processing in Mtb. Ribonucleases (RNases) maintain the cellular RNA pool by RNA processing and degradation. In many bacteria, including the human pathogen Mycobacterium tuberculosis (Mtb), the enzymes mediating several central RNA processing functions are still unknown. Here, we identify the hypothetical Mtb protein Rv2179c as a highly divergent exoribonuclease. Although the primary sequence of Rv2179c has no detectable similarity to any known RNase, the Rv2179c crystal structure reveals an RNase fold. Active site residues are equivalent to those in the DEDD family of RNases, and Rv2179c has close structural homology to Escherichia coli RNase T. Consistent with the DEDD fold, Rv2179c has exoribonuclease activity, cleaving the 3′ single-strand overhangs of duplex RNA. Functional orthologs of Rv2179c are prevalent in actinobacteria and found in bacteria as phylogenetically distant as proteobacteria. Thus, Rv2179c is the founding member of a new, large RNase family with hundreds of members across the bacterial kingdom.
Association between omega-3 fatty acids and serum prostate-specific antigen

ABSTRACT We examined the association between omega-3 fatty acids (O3FAs) and prostate-specific antigen (PSA) in a cross-sectional analysis of 6219 men examined at the Cooper Clinic from 2009 to 2013. We assayed O3FAs from red blood cell membranes and measured PSA levels in study participants. Multiple logistic regression was used to examine the association between O3FAs and PSA. The mean age of study participants was 55.5 years (SD = 9.8) with a mean PSA level of 1.31 ng/mL (SD = 1.5). Unadjusted analyses indicated that there was a slight, direct association with PSA and each of the O3FAs tested. However, after adjusting for age and body mass index (BMI), the associations were reversed but nonsignificant [odds ratio (OR) for PSA > 4 ng/mL: total omega-3 OR = 0.98 per each 1% of total fatty acids, 95% confidence interval (CI) = 0.93–1.03; docosahexaenoic acid OR = 1.01, 95% CI = 0.92–1.11; omega-3 index OR = 0.99, 95% CI = 0.93–1.05). Similar results were obtained after age and BMI adjustment when the omega-3 index was divided into undesirable (0.01–3.99%), intermediate (4.0–7.99%), and desirable ranges ( ≥ 8.0%). Given that the study had >80% power to detect an odds ratio <0.9 or >1.1, we conclude that associations between O3FAs and PSA levels are either nonexistent or quite weak in the population that this healthy sample represents.
Escherichia coli type III secretion system 2 (ETT2) is widely distributed in avian pathogenic Escherichia coli isolates from Eastern China

SUMMARY Pathogens utilize type III secretion systems to deliver effector proteins, which facilitate bacterial infections. The Escherichia coli type III secretion system 2 (ETT2) which plays a crucial role in bacterial virulence, is present in the majority of E. coli strains, although ETT2 has undergone widespread mutational attrition. We investigated the distribution and characteristics of ETT2 in avian pathogenic E. coli (APEC) isolates and identified five different ETT2 isoforms, including intact ETT2, in 57·6% (141/245) of the isolates. The ETT2 locus was present in the predominant APEC serotypes O78, O2 and O1. All of the ETT2 loci in the serotype O78 isolates were degenerate, whereas an intact ETT2 locus was mostly present in O1 and O2 serotype strains, which belong to phylogenetic groups B2 and D, respectively. Interestingly, a putative second type III secretion-associated locus (eip locus) was present only in the isolates with an intact ETT2. Moreover, ETT2 was more widely distributed in APEC isolates and exhibited more isoforms compared to ETT2 in human extraintestinal pathogenic E. coli, suggesting that APEC might be a potential risk to human health. However, there was no distinct correlation between ETT2 and other virulence factors in APEC.
Hospitalizations for Total Hip Arthroplasty after Renal Transplantation in the United States

The national incidence of and factors associated with total hip arthroplasty in renal transplant recipients has not been reported. We conducted an historical cohort study of 42 096 renal transplant recipients in the United States between 1 July 1994 and 30 June 1998. Primary outcomes were associations with hospitalizations for a primary discharge code of total hip arthroplasty (ICD9 procedure code 81.51x) within 3 years after renal transplant using Cox regression. Renal transplant recipients had a cumulative incidence of total hip arthroplasty of 5.1 episodes/1000 person‐years, which is 5–8 times higher than reported in the general population. Avascular necrosis of the hip was the most frequent primary diagnosis associated with total hip arthroplasty in this population (72% of cases). Repeat surgeries were performed in 27% of patients with avascular necrosis, vs. 15% with other diagnoses. Total hip arthroplasty was more frequent in transplant recipients who were older, African American, or who experienced allograft rejection. Mortality after total hip arthroplasty was 0.21% at 30 days and 15% at 3 years, similar to the mortality of all transplant recipients. The most common indication for total hip arthroplasty after renal transplant is avascular necrosis of the hip, in contrast to the general population. Although repeat surgeries are common, total hip arthroplasty is well tolerated and is not associated with increased mortality in this population.