Miracle-dz/UniFAR-FTUs huggingface dataset:
A Whole Genome Screen for Minisatellite Stability Genes in Stationary-Phase Yeast Cells

Repetitive elements comprise a significant portion of most eukaryotic genomes. Minisatellites, a type of repetitive element composed of repeat units 15−100 bp in length, are stable in actively dividing cells but change in composition during meiosis and in stationary-phase cells. Alterations within minisatellite tracts have been correlated with the onset of a variety of diseases, including diabetes mellitus, myoclonus epilepsy, and several types of cancer. However, little is known about the factors preventing minisatellite alterations. Previously, our laboratory developed a color segregation assay in which a minisatellite was inserted into the ADE2 gene in the yeast Saccharomyces cerevisiae to monitor alteration events. We demonstrated that minisatellite alterations that occur in stationary-phase cells give rise to a specific colony morphology phenotype known as blebbing. Here, we performed a modified version of the synthetic genetic array analysis to screen for mutants that produce a blebbing phenotype. Screens were conducted using two distinctly different minisatellite tracts: the ade2-min3 construct consisting of three identical 20-bp repeats, and the ade2-h7.5 construct, consisting of seven-and-a-half 28-bp variable repeats. Mutations in 102 and 157 genes affect the stability of the ade2-min3 and ade2-h7.5 alleles, respectively. Only seven hits overlapped both screens, indicating that different factors regulate repeat stability depending upon minisatellite size and composition. Importantly, we demonstrate that mismatch repair influences the stability of the ade2-h7.5 allele, indicating that this type of DNA repair stabilizes complex minisatellites in stationary phase cells. Our work provides insight into the factors regulating minisatellite stability.
Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley

Significance Archaeological, historic, and molecular studies have indicated that the Fertile Crescent in the Near East is a major center of origin and domestication of cultivated barley. However, growing evidence in recent years supports the theory of a polyphyletic origin of barley. To our knowledge, this is the first attempt using RNA sequencing techniques and genomic similarity analysis to study the domestication of barley. We confirmed the polyphyletic origin of cultivated barley and our results revealed the genomic origin of modern cultivated barley is from both the Near East and Tibet, with different contributions on each chromosome. These findings advance our understanding of the early spread of agrarian culture, and are expected to be of wide interest to evolutionary geneticists and plant breeders. The domestication of cultivated barley has been used as a model system for studying the origins and early spread of agrarian culture. Our previous results indicated that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. Here we reveal multiple origins of domesticated barley using transcriptome profiling of cultivated and wild-barley genotypes. Approximately 48-Gb of clean transcript sequences in 12 Hordeum spontaneum and 9 Hordeum vulgare accessions were generated. We reported 12,530 de novo assembled transcripts in all of the 21 samples. Population structure analysis showed that Tibetan hulless barley (qingke) might have existed in the early stage of domestication. Based on the large number of unique genomic regions showing the similarity between cultivated and wild-barley groups, we propose that the genomic origin of modern cultivated barley is derived from wild-barley genotypes in the Fertile Crescent (mainly in chromosomes 1H, 2H, and 3H) and Tibet (mainly in chromosomes 4H, 5H, 6H, and 7H). This study indicates that the domestication of barley may have occurred over time in geographically distinct regions.
Infant oral health education for pediatric and family practice residents.

PURPOSE The purpose of this study was to investigate whether an infant oral health curriculum implemented in pediatric and family medicine residency programs could improve physicians' oral health knowledge and practice behaviors and promote the age 1 dental visit. METHODS Residents and faculty members completed a baseline current practices survey and knowledge test before receiving a 1- or 2-hour training session followed by a knowledge post-test. Existing well child care forms were updated with oral health prompts to reinforce newly learned skills. At 1-year follow-up (1 YFU), participants completed a current practices survey and knowledge test. In addition to the residency programs, medical students and advanced practice registered nurses participated in baseline data collection, training, and immediate posttest data collection. RESULTS A total of 245 people participated, with 78% trained in person and 22% trained via the Web. Of these, 120 were the targeted residents and faculty-of whom 82% completed the 1 YFU. Practice behaviors improved from baseline to 1 YFU, with only 28% of practitioners at baseline referring children to the dentist at age 1, compared to 73% at 1 YFU (P<.05). Knowledge scores were greater at 1 YFU than at baseline (P<.05), and the mode of training showed no difference in knowledge outcomes. Knowledge and prescribing practices regarding fluoride were poor at baseline and showed limited improvement at 1 YFU. CONCLUSIONS An infant oral health education program can improve physicians' oral health knowledge and behaviors, particularly regarding promoting the age 1 dental visit. Behavior changes regarding fluoride prescribing, however, appear harder to achieve. Web-based training had similar success to in-person training.
A survey on combinatorial optimization in dynamic environments

This survey presents major results and issues related to the study of NPO problems in dynamic environments, that is, in settings where instances are allowed to undergo some modifications over time. In particular, the survey focuses on two complementary frameworks. The first one is the reoptimization framework, where an instance I that is already solved undergoes some local perturbation. The goal is then to make use of the information provided by the initial solution to compute a new solution. The second framework is probabilistic optimization, where the instance to optimize is not fully known at the time when a solution is to be proposed, but results from a determined Bernoulli process. Then, the goal is to compute a solution with optimal expected value.
Misidentification of mucoid variants of Staphylococcus aureus by standard laboratory techniques

Ten atypical strains of Staphylococcus aureus were examined and compared with previously characterized S. aureus strains. Five of the strains were sent to two hospital microbiology laboratories for identification. All of the mucoid strains were misidentified when tested by standardized coagulase, DNase, and mannitol fermentation criteria, as well as by an automated identification method, but were accurately identified by the API system (Analytab Products, Plainview, N.Y.). These results illustrate the possibility of misidentification when reliance is placed on a few key characteristics rather than a thorough characterization of unusual Staphylococcus isolates.
Deterministic (Δ + 1)-Coloring in Sublinear (in Δ) Time in Static, Dynamic and Faulty Networks

In the distributed message passing model a communication network is represented by an n-vertex graph G = (V,E) of maximum degree Δ. Computation proceeds in discrete synchronous rounds consisting of sending and receiving messages and performing local computations. The running time of an algorithm is the number of rounds it requires. In the static setting the network remains unchanged throughout the entire execution. In the dynamic setting the topology of the network changes, and a new solution has to be computed after each change. In the faulty setting the network is static, but some vertices or edges may lose the computed solution as a result of faults. The goal of an algorithm in this setting is fixing the solution. The problems of (Δ + 1)-vertex-coloring and (2Δ - 1)-edge-coloring are among the most important and intensively studied problems in distributed computing. Despite a very intensive research in the last 30 years, no deterministic algorithms for these problems with sublinear (in Δ) time have been known so far. Moreover, for more restricted scenarios and some related problems there are lower bounds of Ω(Δ) [13, 14, 20, 27]. The question of the possibility to devise algorithms that overcome this challenging barrier is one of the most fundamental questions in distributed symmetry breaking [4, 6, 13, 14, 19, 24]. In this paper we settle this question for (Δ + 1)-vertex-coloring and (2Δ - 1)-edge-coloring by devising deterministic algorithms that require O(Δ3/4 log Δ + log* n) time in the static, dynamic and faulty settings. (The term log* n is unavoidable in view of the lower bound of Linial [21]. Moreover, for (1 + o(1))Δ-vertex-coloring and (2 + o(1))Δ-edge-coloring we devise algorithms with Õ(√Δ + log* n) deterministic time. This is roughly a quadratic improvement comparing to the state-of-the-art that requires O(Δ + log* n) time [4, 19, 24]. Our results are actually more general than that since they apply also to a variant of the list-coloring problem that generalizes ordinary coloring. Our results are obtained using a novel technique for coloring partially-colored graphs (also known as fixing). We partition the uncolored parts into a small number of subgraphs with certain helpful properties. Then we color these subgraphs gradually using a technique that employs constructions of polynomials in a novel way. Our construction is inspired by the algorithm of Linial [21] for ordinary O(Δ2)-coloring. However, it is a more sophisticated construction that differs from [21] in several important respects. These new insights in using systems of polynomials allow us to significantly speed up the O(Δ)-coloring algorithms. Moreover, they allow us to devise algorithms with the same running time also in the more complicated settings of dynamic and faulty networks.
Duration of Effect by Injection Volume and Facial Subregion for a Volumizing Hyaluronic Acid Filler in Treating Midface Volume Deficit

BACKGROUND Juvéderm Voluma XC (VYC-20L) is approved in the United States for correction of age-related volume loss in the midface region in adults. OBJECTIVE To characterize the effects of VYC-20L in 3 midface subregions based on injection volumes. METHODS In this single-blind controlled trial, subjects with midface volume deficit received VYC-20L in ≥1 of 3 facial subregions (zygomaticomalar, anteromedial cheek, and submalar), with touch-up treatment available 30 days later. Responders achieved ≥1-point improvement on the Mid-Face Volume Deficit Scale (MFVDS), analyzed by facial subregion and stratified by injection volume quartiles. Subject satisfaction and safety were assessed. RESULTS The treatment arm comprised 235 subjects aged 35 to 65 years. Month 6 MFVDS responder rates were 75.5% for zygomaticomalar, 83.2% for anteromedial cheek, and 76.9% for submalar subregions. Higher responder rates were observed with increasing injection volume quartiles for each subregion. Similar median injection volumes (≈2.0 mL total) of VYC-20L provided correction durations of 15 to 24 months: 24 months for anteromedial cheek, 19 months for zygomaticomalar, and 15 months for submalar subregions. Subject satisfaction was high across injection volume quartiles. No unanticipated treatment-site adverse reactions occurred. CONCLUSION VYC-20L is effective at restoring midface volume, with high subject satisfaction and an acceptable safety profile.
Rule-governed behavior and sensitivity to changing consequences of responding.

Humans were presented with a task that required moving a light through a matrix. Button presses could produce light movements according to a multiple fixed-ratio 18/differential-reinforcement-of-low-rate 6-s schedule, with components alternating every 2 min. Moving the light through the maze earned points worth chances on money prizes. In Experiment 1 four conditions were assessed through between-subject comparisons: minimal instructions, instructions to press rapidly, instructions to press slowly, and instructions that sometimes rapid responding would work while at other times a slow rate would work best. Subjects responded in three successive sessions of 32 min each. The results suggested that instructions affected the nature of the contact made with the programmed consequences and thus subsequent performance. In some cases, responding seemed to result from added contingencies introduced by stating rules. In Experiment 2 the relative contribution of these two effects was assessed by presenting and then withdrawing two lights that had been paired with two specific instructions: "Go Fast" or "Go Slow. " There were three conditions. In one condition, only the Go Fast light was on; in a second, only the Go Slow light was on; and in a third, the lights alternated each minute. In each condition, half the subjects had all instruction lights turned off after the first session. The results once again showed an effect of instructions on contact with the programmed consequences. However, responding sometimes continued in a manner consistent with added contingencies for rule-following even when the programmed consequences had been contacted and would have controlled a different type of responding in the absence of instructions. The relevance of added contingencies for rule-following in determining the effects of explicitly programmed consequences is emphasized.
A Global Expectation–Maximization Approach Based on Memetic Algorithm for Vibration-Based Structural Damage Detection

This paper proposes a novel unsupervised damage detection approach based on a memetic algorithm that establishes the normal or undamaged condition of a structural system as data clusters through a global xpectation–maximization technique, using only damage-sensitive features extracted from output-only vibration measurements. The health state is then discriminated by considering the Mahalanobis squared distance between the learned clusters and a new observation. The proposed approach is compared with state-of-the-art ones by taking into account real-world data sets from the Z-24 Bridge (Switzerland), where several damage scenarios were performed. The results indicated that the proposed approach can be applied in structural health monitoring applications where life safety, economic, and reliability issues are the most important motivations to consider.
Futile Interhospital Transfer for Endovascular Treatment in Acute Ischemic Stroke: The Madrid Stroke Network Experience

Background and Purpose— The complexity of endovascular revascularization treatment (ERT) in acute ischemic stroke and the small number of patients eligible for treatment justify the development of stroke center networks with interhospital patient transfers. However, this approach might result in futile transfers (ie, the transfer of patients who ultimately do not undergo ERT). Our aim was to analyze the frequency of these futile transfers and the reasons for discarding ERT and to identify the possible associated factors. Methods— We analyzed an observational prospective ERT registry from a stroke collaboration ERT network consisting of 3 hospitals. There were interhospital transfers from the first attending hospital to the on-call ERT center for the patients for whom this therapy was indicated, either primarily or after intravenous thrombolysis (drip and shift). Results— The ERT protocol was activated for 199 patients, 129 of whom underwent ERT (64.8%). A total of 120 (60.3%) patients required a hospital transfer, 50 of whom (41%) ultimately did not undergo ERT. There were no differences in their baseline characteristics, the times from stroke onset, or in the delays in interhospital transfers between the transferred patients who were treated and those who were not treated. The main reasons for rejecting ERT after the interhospital transfer were clinical improvement/arterial recanalization (48%) and neuroimaging criteria (32%). Conclusions— Forty-one percent of the ERT transfers were futile, but none of the baseline patient characteristics predicted this result. Futility could be reduced if repetition of unnecessary diagnostic tests was avoided.
CLINICAL STUDY: Cloninger’s typology and treatment outcome in alcohol‐dependent subjects during pharmacotherapy with naltrexone

Naltrexone is an opiate receptor antagonist mainly at the µ‐receptor that is thought to reduce the positively reinforcing, pleasurable effects of alcohol and to reduce craving. An increase in time to first relapse to heavy drinking has been the most consistent finding obtained with naltrexone, although not all trials including two of the largest have been positive. Inconsistent outcome data suggest that effectiveness varies among different subgroups of patients. This paper re‐evaluates recent data on the effectiveness of naltrexone in subjects differentiated according to Cloninger Type I and II. Moreover, it combines and cross‐validates results of two recent European studies that found naltrexone treatment more beneficial in alcohol‐dependent patients with early age at onset of drinking problems (Cloninger Type II). It is discussed whether especially these subjects should be targeted for pharmacological relapse prevention treatment with naltrexone.
Indoor Position Tracking Using Multiple Optical Receivers

An indoor positioning system is a key component in enabling location-based services in future wireless networks. The need for a highly accurate indoor positioning system is rapidly increasing. In the past couple of years, several positioning systems based on visible light communications that achieve good positioning accuracy have been proposed. Some of these systems are based on assumptions such as complete knowledge of the height of the receiver, and exact alignment of the transmitter and receiver normals to the normal of the ceiling. Some other systems do not support user mobility because they require a user to vary the receiver orientation at a fixed location. Another common assumption is that the transmitters are at the same height from the ground. In order to support user mobility, this paper proposes a novel positioning system using multiple optical receivers that provides coordinates and an orientation of the mobile receiver. The remarkable features of the system are as follows: 1) the receiver can be mobile; 2) the positioning is done within 2.5 ms in our experimental setup; 3) the heights of the transmitters need not be the same; 4) the receiver's height need not be known; and 5) the receiver's normal need not be aligned with those of the transmitters. Experimental results show that mean position errors of less than 0.06 m is achievable even when the average receiver speed is 1.3 m/s.
The Inflammatory C-Reactive Protein is Increased in Both Liver and Adipose Tissue in Severely Obese Patients Independently from Metabolic Syndrome, Type 2 Diabetes, and NASH

OBJECTIVE:C-Reactive Protein (CRP), a nonspecific marker of inflammation that is moderately elevated in obesity, metabolic syndrome (MS), and type 2 diabetes, has been proposed as a surrogate marker of nonalcoholic steatohepatitis (NASH). Its clinical usefulness in the diagnosis of NASH was evaluated in severely obese patients without or with MS, diabetes, and NASH and the potential roles of the liver and of the adipose tissue in CRP production were characterized.METHODS:Severely obese patients without NASH (without MS [N = 13], with MS [N = 11], or with MS and diabetes [N = 7]) and with NASH (without [N = 8] or with [N = 7] MS) were studied. For each patient, liver and adipose tissue biopsies were collected during a bariatric surgery and were used to determine the CRP gene expression by real-time PCR. The role of interleukin-6 (IL6) and lipopolysaccharide in CRP expression was also evaluated in subcutaneous adipose tissue obtained during cosmetic abdominoplasty.RESULTS:Plasma CRP levels were elevated in severely obese patients independently from the presence or absence of MS, diabetes, or NASH. CRP gene expression was not only increased in livers but also in adipose tissues of obese patients compared with controls subjects. In human adipose tissue, CRP mRNA levels were positively correlated with those of IL-6 and the CRP expression was enhanced in vitro by IL-6 and lipopolysaccharide.CONCLUSION:Plasma CRP levels are not predictive of the diagnosis of NASH in severely obese patients. The liver but also the adipose tissue can produce CRP, a process which could be dependent on IL6. Therefore, both tissues might contribute to the elevated plasma CRP levels found in obesity. In addition, the large amount of body fat may well produce an important part of the circulating CRP, further limiting its clinical usefulness in the evaluation of NASH in severely obese patients.
The Practicability of a Novel Prognostic Index (PI) Model and Comparison with Nottingham Prognostic Index (NPI) in Stage I–III Breast Cancer Patients Undergoing Surgical Treatment

Background Previous studies have indicated the prognostic value of various laboratory parameters in cancer patients. This study was to establish a prognostic index (PI) model for breast cancer patients based on the potential prognostic factors. Methods A retrospective study of 1661 breast cancer patients who underwent surgical treatment between January 2002 and December 2008 at Sun Yat-sen University Cancer Center was conducted. Multivariate analysis (Cox regression model) was performed to determine the independent prognostic factors and a prognostic index (PI) model was devised based on these factors. Survival analyses were used to estimate the prognostic value of PI, and the discriminatory ability of PI was compared with Nottingham Prognostic Index (NPI) by evaluating the area under the receiver operating characteristics curves (AUC). Results The mean survival time of all participants was 123.6 months. The preoperative globulin >30.0g/L, triglyceride >1.10mmol/L and fibrinogen >2.83g/L were identified as risk factors for shorter cancer-specific survival. The novel prognostic index model was established and enrolled patients were classified as low- (1168 patients, 70.3%), moderate- (410 patients, 24.7%) and high-risk groups (83 patients, 5.0%), respectively. Compared with the low-risk group, higher risks of poor clinical outcome were indicated in the moderate-risk group [Hazard ratio (HR): 1.513, 95% confidence interval (CI): 1.169–1.959, p = 0.002] and high-risk group (HR: 2.481, 95%CI: 1.653–3.724, p< 0.001). Conclusions The prognostic index based on three laboratory parameters was a novel and practicable prognostic tool. It may serve as complement to help predict postoperative survival in breast cancer patients.