Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct Chloroplast Sequencing: Comparison of Sequencing Platforms and Analysis Tools for Whole Chloroplast Barcoding

Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina) and Ion Torrent (Life Technology) sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare). Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels) between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.
Optimal Stochastic Parameter Design for Estimation Problems

In this study, the aim is to perform optimal stochastic parameter design in order to minimize the cost of a given estimator. Optimal probability distributions of signals corresponding to different parameters are obtained in the presence and absence of an average power constraint. It is shown that the optimal parameter design results in either a deterministic signal or a randomization between two different signal levels. In addition, sufficient conditions are obtained to specify the cases in which improvements over the deterministic parameter design can or cannot be achieved via the stochastic parameter design. Numerical examples are presented in order to provide illustrations of theoretical results.
Meta-analysis: Age and Effectiveness of Prophylactic Implantable Cardioverter-Defibrillators

BACKGROUND Implantable cardioverter-defibrillators (ICDs) for the primary prevention of sudden cardiac death have been proven effective in several clinical trials. PURPOSE To summarize evidence about the effectiveness of ICDs versus standard medical therapy for the primary prevention of sudden cardiac death in different age groups of patients with severe left ventricular dysfunction. DATA SOURCES MEDLINE, Embase, CENTRAL, BioMed Central, Cardiosource, ClinicalTrials.gov, and ISI Web of Science (January 1970 to April 2010) were searched with no language restrictions. STUDY SELECTION Two independent reviewers screened titles and abstracts to identify randomized, controlled trials of prophylactic ICD versus medical therapy in patients with severe left ventricular dysfunction that provided data about mortality outcomes for different age groups. DATA EXTRACTION Two independent reviewers assessed risk for bias of trials and extracted patient and study characteristics and hazard ratios (HRs) relevant to all-cause mortality. DATA SYNTHESIS Five trials (MADIT-II, DEFINITE, DINAMIT, SCD-HeFT, and IRIS) that enrolled 5783 patients (44% were elderly) were included. The primary analysis, which excluded the 2 trials enrolling patients early after acute myocardial infarction (DINAMIT and IRIS), found that prophylactic ICD therapy reduced mortality in younger patients (HR, 0.65 [95% CI, 0.50 to 0.83]; P < 0.001). A smaller survival benefit was found in elderly patients (HR, 0.75 [95% CI, 0.61 to 0.91]) that was not confirmed when MADIT-II patients older than 70 years were excluded or when data from DINAMIT and IRIS were included [corrected]. LIMITATIONS Four potentially eligible trials were not included in the meta-analysis because mortality data by age group were not available. Adjustment for differences in comorbid conditions and medical therapies among patients enrolled in the trials was not possible. CONCLUSION Available data suggest that prophylactic ICD therapy may be less beneficial for elderly patients with severe left ventricular dysfunction than for younger patients [corrected]. PRIMARY FUNDING SOURCE None.
Bankruptcy in groups

We examine bankruptcy within business groups. Groups have incentives to support financially distressed subsidiaries, as the bankruptcy of a subsidiary may impose severe costs on the group as a whole. This is in part because, in several countries, bankruptcy courts often “pierce the corporate veil” and hold groups liable for their distressed subsidiaries’ obligations as if they were their own. Using a large cross-country sample of group-affiliated firms, we show that, by reallocating resources within the corporate structure, business groups actively manage intra-group credit risk to prevent costly within-group insolvencies. Moreover, we document that recent regulatory changes in the approval and disclosure of related party transactions are costly for business groups in that they constrain their ability to shield their subsidiaries from credit-risk shocks. Our study informs the current regulatory debate on related party transactions by highlighting an important cost of anti-self-dealing regulation.
Value of Urinary Albumin-to-Creatinine Ratio as a Predictor of Type 2 Diabetes in Pre-Diabetic Individuals

OBJECTIVE—The albumin-to-creatinine ratio (ACR) reflects urinary albumin excretion and is increasingly being accepted as an important clinical outcome predictor. Because of the great public health need for a simple and inexpensive test to identify individuals at high risk for developing type 2 diabetes, it has been suggested that the ACR might serve this purpose. We therefore determined whether the ACR could predict incident diabetes in a well-characterized cohort of pre-diabetic Americans. RESEARCH DESIGN AND METHODS—A total of 3,188 Diabetes Prevention Program (DPP) participants with a mean BMI of 34 kg/m2 and elevated fasting glucose, impaired glucose tolerance, and baseline urinary albumin excretion measurements were followed for incident diabetes over a mean of 3.2 years. RESULTS—Of the participants, 94% manifested ACR levels below the microalbuminuria range and 21% ultimately developed diabetes during follow-up. Quartiles of ACR (median [range] within quartiles: 1, 3.0 [0.7–3.7]; 2, 4.6 [3.7–5.5]; 3, 7.1 [5.5–9.7]; and 4, 16.5 [9.7–1,578]) were positively associated with age, markers of adiposity and insulin secretion and resistance, blood pressure, and use of antihypertensive agents with antiproteinuric effects and inversely related to male sex and serum creatinine. An elevated hazard rate for developing diabetes with doubling of ACR disappeared after adjustment for covariates. Within the DPP intervention groups (placebo, lifestyle, and metformin), we found no consistent trend in incident diabetes by quartile or decile of ACR. CONCLUSIONS—An ACR at levels below the microalbuminuria range does not independently predict incident diabetes in adults at high risk of developing type 2 diabetes.
Comparison of the ocular surface changes following the use of two different prostaglandin F2α analogues containing benzalkonium chloride or polyquad in rabbit eyes

Abstract Objective: The aim of this study is to compare the effect of prostaglandin analogues preserved with either 0.015% or 0.001% benzalkoium chloride (BAK); or 0.001% polyquad (PQ) on the ocular surface of rabbit eyes. Methods: Forty white rabbits were randomized to receive four-times daily instillation of either 0.0015% tafluprost (TF) preserved with 0.001% BAK (TF-BAK); 0.004% travoprost (TR) with 0.015% BAK (TR-BAK) or 0.001% PQ (TR-PQ); or preservative-free artificial tears in one eye for a 4-week period. Tear samples collected from the 40 rabbits were analyzed by enzyme-linked immunosorbent assays (ELISA) to identify the presence of inflammatory cytokines: interleukin (IL)-1β and IL-6 on day 14. Subsequently, harvested cornea and bulbar conjunctiva were evaluated using light and transmission electron microscopy (TEM). Results: IL-6 was significantly increased in TF-BAK and TR-BAK groups compared to controls and TR-PQ group (p = 0.005); however, IL-1β level was not significantly different among four groups (p = 0.360). Rabbits treated with TR-BAK showed decreased goblet cell density of bulbar conjunctiva and increased pyknotic change and vacuolization of corneal epithelial cells on light microscopy; similar change occurred but was less severe in TF-BAK group. The TR-PQ group showed similar results as the controls. The destruction of the microvillar architecture of bulbar conjunctiva and cornea was most prominent in the TR-BAK group. Conclusions: Preservatives included in the anti-glaucoma eye-drops showed different ocular surface changes according to the concentration and type in the rabbits. Prostaglandin analogues preserved with higher level of BAK may cause more harmful effects on the ocular surface than PQ-preserved medications.
Investigating Facial Behavior Indicators of Suicidal Ideation

Suicide is the deliberate self-inflicted act with the intent to end one’s own life. It reflects both profound personal suffering and societal failure. While certain suicide risk factors are well understood, predicting suicide attempts remains a very challenging problem. In this paper, we investigate non-verbal facial behaviors to discriminate among control, mentally ill, and suicidal patients. For this task, we used a balanced corpus containing interviews of male and female patients with and without suicide ideation and/or mental health disorders from 3 different hospitals. In our experiments, we explored smiling, frowning, eyebrow raising, and head motion behaviors. We investigated both the occurrence of these behaviors and also how they were conducted. We found that facial behavior descriptors such as the percentage of smiles involving the contraction of the orbicularis oculi muscles (Duchenne smiles) had statistically significant differences between the suicidal and nonsuicidal groups. Our experiments also demonstrated that the stage of the interview in which these facial behaviors occur impacts their discriminative power.
Emergency Department Visits and Use of Outpatient Physician Services by Adults with Developmental Disability and Psychiatric Disorder

Objective: To compare the emergency department (ED), primary, and psychiatric care visit rates associated with the presence and absence of a developmental disability (DD) and a mental illness. Method: This is a population-based study comparing Ontario adults, with and without DDs and mental illnesses, in terms of rates of primary, psychiatric, and ED care, from April 2007 to March 2009. Results: In Ontario, 45% of adults with a DD received a psychiatric diagnosis during a 2-year period, and 26% of those with a psychiatric diagnosis were classified as having a serious mental illness (SMI), compared with 8% of those with a psychiatric diagnosis but no DD. People with DDs had an increased likelihood of psychiatric and ED visits. Patients with SMIs and DDs had the highest rates of such visits. Conclusions: People with more severe impairments had the greatest likelihood of ED visits, despite access to outpatient services, suggesting that outpatient care (primary and psychiatric), as currently delivered, may not be adequate to meet their complex needs.
Contrasting lever-press avoidance behaviors of spontaneously hypertensive and normotensive rats (Rattus norvegicus).

Lever-press avoidance performances of Spontaneously Hypertensive (SHR) and Wistar-Kyoto (WKY) rats were observed in two experiments. The first compared them at shock intensities of 1 or 2 mA. The SHRs had the highest percentage of avoidances, made the most coping responses (avoidances plus escapes), and received the fewest shocks (ps less than .05). They also had shorter avoidance and initial-escape latencies (ps less than .05). In the second experiment these strains were trained with signal-shock intervals that produce good (60 s) or poor (10 s) avoidance acquisition. Analysis of the Strain x Conditions x Blocks interaction showed that SHRs performed better with the longer interval (p less than .05), whereas WKYs' performance was similar with both (p greater than .05). Thus WKYs differed from all other strains previously exposed to these conditions. The findings are interpreted in terms that emphasize the SHRs' tendency to move, compared with the WKYs' tendency to freeze in response to aversive stimuli, rather than characterizing SHRs as hyperreactive.
Catecholamine and Volume Therapy for Cardiac Surgery in Germany – Results from a Postal Survey

Background Management of cardiac surgery patients is a very standardized procedure in respective local institutions. Yet only very limited evidence exists concerning optimal indication, safety and efficacy of hemodynamic monitoring catecholamine and fluid therapy. Methods Between April and May 2013, all 81 German anaesthesia departments involved in cardiac surgery care were asked to participate in a questionnaire addressing the institutional specific current practice in hemodynamic monitoring, catecholamine and volume therapy. Results 51 (63%) questionnaires were completed and returned. All participating centers used basic hemodynamic monitoring (i.e. invasive arterial blood pressure and central venous pressure), supplemented by transesophageal echocardiography. Pulmonary arterial catheter and calibrated trend monitoring devices were also routinely available. In contrast, non-calibrated trend monitoring and esophageal doppler ultrasound devices were not commonly in use. Cerebral oximetry is increasingly emerging, but lacks clear indications. The majority of patients undergoing cardiac surgery, especially in university hospitals, required catecholamines during perioperative care, In case of low cardiac output syndrome, dobutamine (32%), epinephrine (30%) or phosphodiesterase inhibitors (8%) were first choice. In case of hypotension following vasoplegia, norepinephrine (96%) represented the most common catecholamine. 88% of the participating centers reported regular use of colloid fluids, with hydroxyethyl starches (HES) being first choice (64%). Conclusions Choice of hemodynamic monitoring is homogenous throughout German centers treating cardiac surgery patients. Norepinephrine is the first line catecholamine in cases of decrease in peripheral vascular resistance. However, catecholamine choice for low cardiac output syndrome varies considerably. HES was the primary colloid used for fluid resuscitation. After conduct of this survey, HES use was restricted by European regulatory authorities in critically ill patients and should only be considered as second-line fluid in surgical patients without renal impairment or severe coagulopathy. Large clinical studies addressing catecholamine and fluid therapy in cardiac surgery patients are lacking.
DIRECTORYLESS SHARED MEMORY COHERENCE USING EXECUTION MIGRATION

We introduce the concept of deadlock-free migration-based coherent shared memory to the NUCA family of architectures. Migration-based architectures move threads among cores to guarantee sequential semantics in large multicores. Using a execution migration (EM) architecture, we achieve performance comparable to directory-based architectures without using directories: avoiding automatic data replication significantly reduces cache miss rates, while a fast network-level thread migration scheme takes advantage of shared data locality to reduce remote cache accesses that limit traditional NUCA performance. EM area and energy consumption are very competitive, and, on the average, it outperforms a directory-based MOESI baseline by 1.3 and a traditional S-NUCA design by 1.2 . We argue that with EM scaling performance has much lower cost and design complexity than in directorybased coherence and traditional NUCA architectures: by merely scaling network bandwidth from 256 to 512 bit flits, the performance of our architecture improves by an additional 13%, while the baselines show negligible improvement.
Phenytoin Metabolism in the Cat After Long‐Term Oral Administration

Summary: The metabolism of sodium phenytoin (PHT) in the cat was studied by gas‐liquid chromatographic analyses of the drug and its metabolites extracted from plasma, urine, and feces during a 5‐month course of daily oral administration. Plasma PHT levels of 15–18 μg/ml were observed. Urine contained 5‐(4‐hydroxyphenyl)‐5‐phenylhydantoin, 5‐(3,4‐dihydroxy‐1,5‐cyclohexadien‐1‐yl)‐5‐phenylhydantoin, 1‐deoxy‐1‐(5,5‐diphenylhydantoin‐3‐yl)‐β‐d‐glucopyranuronate, and unmetabolized PHT. Large quantities of PHT (32–63% of the daily dose) were observed in feces. We suggest that gastrointestinal malabsorption, extensive N‐glucuronidation, and limited hydroxylation determine the fate of orally administered PHT in the cat. This is not the case in humans.
Speed-Constrained Tuning for Statistical Machine Translation Using Bayesian Optimization

We address the problem of automatically finding the parameters of a statistical machine translation system that maximize BLEU scores while ensuring that decoding speed exceeds a minimum value. We propose the use of Bayesian Optimization to efficiently tune the speed-related decoding parameters by easily incorporating speed as a noisy constraint function. The obtained parameter values are guaranteed to satisfy the speed constraint with an associated confidence margin. Across three language pairs and two speed constraint values, we report overall optimization time reduction compared to grid and random search. We also show that Bayesian Optimization can decouple speed and BLEU measurements, resulting in a further reduction of overall optimization time as speed is measured over a small subset of sentences.
Purification of cachectin, a lipoprotein lipase-suppressing hormone secreted by endotoxin-induced RAW 264.7 cells

Previous studies have indicated that endotoxin and other bacterial and protozoal products can stimulate macrophages to produce a factor that can suppress the activity of the enzyme lipoprotein lipase (LPL), in vivo and in vitro. In the present report we describe the purification of this factor, cachectin, to apparent homogeneity from the conditioned medium of endotoxin-stimulated RAW 264.7 cells. The isolated protein has an isoelectric point of 4.7 and a subunit molecular weight of 17,000. Although cachectin's isoelectric point and molecular weight are similar to those described for interleukin 1, pure cachectin has no leukocyte-activating factor (LAF) activity. Cachectin at a concentration of 10(-11) M has the ability to suppress the LPL activity of the 3T3-L1 adipocyte cell line by 80%. Binding studies using radio- labeled cachectin and 3T3-L1 adipocytes and C2 myotubules revealed approximately 10(4) high-affinity receptors per cell on both cell types (Ka, 3 X 10(9]. Cachectin receptors were also present on liver membranes but were absent on erythrocytes and lymphocytes. The isolation of cachectin and characterization of its receptor should facilitate further investigations into the role of cachectin and other macrophage mediators in the metabolic derangements that occur during infection and cachexia.
The Impact of Body Mass Index on Mortality After Stroke

Background and Purpose— Little is known about the contribution of obesity to the higher mortality risk among stroke survivors. We assessed the independent association between body mass index (BMI) and mortality among stroke survivors. Methods— Cross-sectional and prospective data from a nationally representative survey of noninstitutionalized civilian U.S. population aged 25 or older (n=20 050) with a baseline history of stroke (n=644) followed up from survey participation (1988–1994) through mortality assessment in 2000. Relationships between BMI and mortality attributable to all causes or cardiovascular causes were examined after adjusting for established prognosticators after stroke. Results— Stroke survivors were more likely to be overweight (BMI 25 to 29 kg/m2) or obese (BMI ≥30 kg/m2) than those without stroke (64.3% versus 53.2%, P=0.003). In multivariable analysis, overall risk for all-cause mortality increased per kg/m2 of higher BMI (P=0.030), but an interaction between age and BMI (P=0.009) revealed that the association of higher BMI with mortality risk was strongest in younger individuals and declined linearly with increasing age, such that in the elderly, overweightness and obesity had a protective effect. The results were similar for the cardiovascular mortality outcome. Conclusions— Higher BMI after stroke is associated with a greater risk of all-cause and cardiovascular death among younger individuals. Younger stroke survivors may especially benefit from more vigorous efforts to monitor and treat obesity.
Linked Lives: Adult Children's Problems and Their Parents' Psychological and Relational Well-being

This study examined associations between adult children's cumulative problems and their parents' psychological and relational well-being, as well as whether such associations are similar for married and single parents. Regression models were estimated using data from 1,188 parents in the 1995 National Survey of Midlife in the United States whose youngest child was at least 19 years old. Participants reporting children with more problems indicated moderately poorer levels of well-being across all outcomes examined. Single parents reporting more problems indicated less positive affect than a comparable group of married parents, but married parents reporting more problems indicated poorer parent-child relationship quality. Findings are congruent with the family life course perspective, conceptualizing parents and children as occupying mutually influential developmental trajectories. Distressing circumstances—such as substance abuse, divorce, and long-term unemployment— are not uncommon among adults in the United Empirical studies have indicated that these problems not only jeopardize the well-being of adults who directly experience them but also endanger the well-being of distressed individuals' family members, including their children and partners (e. There has been little empirical investigation, however, of the extent to which adults' problems affect other family members, in particular individuals' parents. Guided by a family life course perspective, this study investigated linkages between adult chil-dren's cumulative number of problems and their parents' well-being. More specifically, we used data from the 1995 National Survey of Midlife in the United States (MIDUS) to test the hypothesis that parents of adult children experiencing more types of problems would report poorer psychological well-being (more negative affect, less positive affect, and less self-acceptance) and poorer rela-tional well-being (poorer parent-child relationship quality and more family relationship strain) than parents of adult children experiencing fewer types of problems. We also examined whether being married (vs. single) moderates these associations, hypothesizing that being married would help to buffer parents from the negative implications of their adult children's greater number of problems. THEORETICAL AND EMPIRICAL BACKGROUND This study draws on the family life course perspective as a theoretical framework that orients