Miracle-dz/UniFAR-FTUs huggingface dataset:
A key role for the 12-hydroxy group in the negative ion fragmentation of unconjugated C24 bile acids

Host-gut microbial interactions contribute to human health and disease states and an important manifestation resulting from this co-metabolism is a vast diversity of bile acids (BAs). There is increasing interest in using BAs as biomarkers to assess the health status of individuals, and therefore, an increased need for their accurate separation and identification. In this study, the negative ion fragmentation behaviors of C24 BAs were investigated by UPLC-ESI-QTOF-MS. The step-by-step fragmentation analysis revealed a distinct fragmentation mechanism for the unconjugated BAs containing a 12-hydroxyl group. The unconjugated BAs lacking 12-hydroxylation fragmented via dehydration and dehydrogenation. In contrast, the 12-hydroxylated ones, such as deoxycholic acid (DCA) and cholic acid (CA), employed dissociation routes including dehydration, loss of carbon monoxide or carbon dioxide, and dehydrogenation. All fragmentations of the 12-hydroxylated unconjugated BAs, characterized by means of stable isotope labeled standards, were associated with the rotation of the carboxylate side-chain and the subsequent rearrangements accompanied with proton transfer between 12-hydroxyl and 24-carboxyl groups. Compared to DCA, CA underwent further cleavages of the steroid skeleton. Accordingly, the effects of stereochemistry on the fragmentation pattern of CA were investigated using its stereoisomers. Based on the knowledge gained from the fragmentation analysis, a novel BA, 3 β , 7 β , 12 α -trihydroxy-5 β -cholanic acid, was identified in the postprandial urine samples of patients with nonalcoholic steatohepatitis. The analyses used in this study may contribute to a abstract Bile acids (BAs) are the amphipathic products of cholesterol metabolism in vertebrates 1 . They play irreplaceable roles in solubilizing lipids and fat-soluble vitamins 2 , eliminating catabolites such as bilirubin, and aiding in the reduction of the bacteria populations in the biliary tract and small intestine 3 . The physiological role of BAs as important metabolic signaling molecules that modulate lipid, glucose, and energy metabolism has also gained a lot of recognition 4 . Because of an enterohepatic circulation driven by a series of membrane transporters 5 , composition of the human BA pool is entangled with a complex host-gut microbial co-metabolism 6 . In humans, the primary BAs, cholic acid (CA), chenodeoxycholic acid (CDCA) and their taurine and glycine conjugates, are synthesized via cytochrome P450-mediated oxidation of cholesterol through a multi-step process 7 . They are secreted into the gallbladder where they are stored until postprandial release into the intestine. The secondary BAs are formed in the intestine by a variety of reactions carried out by the gut microbiota, including deconjugation, 7-dehydroxylation, dehydrogenation and epimerization of hydroxyl groups. The majority (>95%) of both the primary and secondary BAs is reabsorbed by the intestine and returned to the liver where some of them undergo sulfation and glucuronidation 8,9 .
Sources of the Family Income Differentials among Hispanics, Blacks, and White Non-Hispanics

Data from the 1976 Survey of Income and Education are used to analyze the family income differentials among the five major Hispanic-American groups (Mexicans, Puerto Ricans, Cubans, Central and South Americans, and "other Spanish"), black non-Hispanics, and white non-Hispanics. Total family income is first classified by its four major sources: earnings of a male head, earnings of a wife or female head, earnings of other family members, and property or transfer income. Next, each potential source of intergroup differences is analyzed for male earnings and then for female earnings: differences in family structure, labor force participation, weeks employed, hours worked per week, and wage rates, For each factor, the ratio of each minority group's average value to that of white non-Hispanics is computed to determine where the overall income gaps arise. In order to adjust for group differences in demographic composition, Fisher's ideal index is also computed for the factors exhibiting sizable gaps.
Impaired Executive Control Is Associated with a Variation in the Promoter Region of the Tryptophan Hydroxylase 2 Gene

Current models of attention describe attention not as a homogenous entity but as a set of neural networks whose measurement yields a set of three endophenotypesalerting, orienting, and executive control. Previous findings revealed different neuroanatomical regions for these subsystems, and data from twin studies indicate differences in their heritability. The present study investigated the molecular genetic basis of attention in a sample of 100 healthy subjects. Attention performance was assessed with the attention network test that distinguishes alerting, orienting, and executive control (conflict) using a simple reaction time paradigm with different cues and congruent and incongruent flankers. Two gene loci on candidate genes for cognitive functioning, the functional catechol-O-methyltransferase (COMT) VAL158MET and the tryptophan hydroxylase 2 (TPH2) 703 G/T promoter polymorphism, were tested for possible associations with attention. COMT is involved in the catabolism of dopamine, and TPH is the rate-limiting enzyme for serotonin synthesis. Results showed no effect of the COMT polymorphism on attention performance. However, the TT genotype of TPH2 03 G/T was significantly associated with more errors (a possible indicator of impaired impulse control; p = .001) and with decreased performance in executive control (p = .001). This single-nucleotide polymorphism on the TPH2 gene explained more than 10% of the variance in both indicators of attention stressing the role of the serotonergic system for cognitive functions.
Recommending API Usages for Mobile Apps with Hidden Markov Model

Mobile apps often rely heavily on standard API frameworks and libraries. However, learning to use those APIs is often challenging due to the fast-changing nature of API frameworks and the insufficiency of documentation and code examples. This paper introduces DroidAssist, a recommendation tool for API usages of Android mobile apps. The core of DroidAssist is HAPI, a statistical, generative model of API usages based on Hidden Markov Model. With HAPIs trained from existing mobile apps, DroidAssist could perform code completion for method calls. It can also check existing call sequences to detect and repair suspicious (i.e. unpopular) API usages.
An Efficient Formulation of Off-line Model Predictive Control for Nonlinear Systems Using Polyhedral Invariant Sets

In this research, an efficient formulation of off-line model predictive control for nonlinear systems is presented. The nonlinear systems are reformulated as linear parameter varying systems so their complexity is reduced without any loss of generality. The on-line computational burdens are decreased by pre-computing off-line the sequences of explicit control laws corresponding to the sequences of polyhedral invariant sets. At each sampling time, the current state and the scheduling parameter are measured. The real-time control law is then calculated by linear interpolation between the pre-computed control laws. The results indicate that the proposed algorithm can achieve better control performance compared to the previously developed off-line robust model predictive control algorithm because the scheduling parameter is incorporated into the controller design
Internal Validation of the Sepsis in Obstetrics Score to Identify Risk of Morbidity From Sepsis in Pregnancy.

OBJECTIVE To prospectively validate the Sepsis in Obstetrics Score, a pregnancy-specific sepsis scoring system, to identify risk for intensive care unit (ICU) admission for sepsis in pregnancy. METHODS This is a prospective validation study of the Sepsis in Obstetrics Score. The primary outcome was admission to the ICU for sepsis. Secondary outcomes included admission to a telemetry unit and time to administration of antibiotic therapy. We evaluated test characteristics of a predetermined score of 6 or greater. RESULTS Between March 2012 and May 2015, 1,250 pregnant or postpartum women presented to the emergency department and met systemic inflammatory response syndrome criteria. Of those, 425 (34%) had a clinical suspicion or diagnosis of an infection, 14 of whom (3.3%) were admitted to the ICU. The Sepsis in Obstetrics Score had an area under the curve of 0.85 (95% CI 0.76-0.95) for prediction of ICU admission for sepsis. This is within the prespecified 15% margin of the area under the curve of 0.97 found in the derivation cohort. A score of 6 or greater had a sensitivity of 64%, specificity of 88%, positive predictive value of 15%, and negative predictive value of 98.6%. Women with a score 6 or greater were more likely to be admitted to the ICU (15% compared with 1.4%, P<.01), admitted to a telemetry unit (37.3% compared with 7.2%, P<.01), and have antibiotic therapy initiated (90% compared with 72.9%, P<.01), initiated more quickly (3.2 compared with 3.7 hours, P=.03), although not within 1 hour (5.6 compared with 3.4%, P=.44). CONCLUSION The Sepsis in Obstetrics Score is a validated pregnancy-specific score to identify risk of ICU admission for sepsis with the threshold score of 6 having a negative predictive value of 98.6%. Adherence to antibiotic administration guidelines is poor.
Perceived organizational membership: An aggregate framework representing the employee-organization relationship.

Organizational scholars have examined the relational ties between employees and organizations, often focusing on specific facets of the relationship. However, this approach has not generated an overall representation of the employee–organization relationship, nor has it facilitated the identification of interrelationships among the concepts. This paper seeks to address these two issues by developing an integrative framework labeled perceived organizational membership. Perceived organizational membership is proposed to be an aggregate multidimensional construct reflecting employees' perceptions of their relationship with their employing organization, and its three underlying dimensions (need fulfillment, mattering, and belonging) offer a framework for categorizing and understanding relational tie concepts, both separately and in combination with one another. Drawing from the community psychology literature (McMillan & Chavis, 1986) as well as Graham's (1991) early work on organizational citizenship, we identify perceived organizational membership's underlying motives and the mechanisms through which they influence the construct, demonstrate how specific relational tie subdimensions fit with the more general construct, and develop propositions regarding relationships among the dimensions and the specific relational tie subdimensions. Finally, we discuss the benefits of the framework, including its ability to allow researchers to better understand both specific relational tie concepts as well as the overall employee–organization relationship. Copyright © 2003 John Wiley & Sons, Ltd.
Binding of Trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis

In Drosophila, the maintenance of developmentally important transcription patterns is controlled at the level of chromatin structure. The Polycomb group (PcG) and trithorax group (trxG) genes encode proteins involved in chromatin remodelling. PcG genes have been proposed to act by packaging transcriptional repressed chromosomal domains into condensed heterochromatin‐like structures. Some of the trxG proteins characterized so far are members of chromatin opening complexes (e.g. SWI/SNF and GAGA/NURF) which facilitate binding of transcription factors and components of the basal transcriptional machinery. Genetic and biochemical data suggest that these two groups of regulatory factors may act through a common set of DNA elements. In the present study, we have investigated the binding of Trithorax (TRX) and Polycomb (PC) protein in the bithorax complex (BX‐C) during embryogenesis. In addition, we have identified the minimal fragments from the Ultrabithorax (Ubx) regulatory region that are capable of recruiting TRX to chromosomal sites containing them. Comparative analysis of the binding of the two proteins shows that TRX and PC bind target sequences (PcG‐regulated elements, PREs) by cellular blastoderm, when BX‐C transcription begins. At the same stage, TRX but not PC is strongly associated with core promoters. Later, at germ band extension, the time of derepression in Polycomb mutants, PC binding is also detected outside core PREs and additionally binds to the fragments containing promoters.
Phage Display–Mediated Discovery of Novel Tyrosinase-Targeting Tetrapeptide Inhibitors Reveals the Significance of N-Terminal Preference of Cysteine Residues and Their Functional Sulfur Atom

Tyrosinase, a key copper-containing enzyme involved in melanin biosynthesis, is closely associated with hyperpigmentation disorders, cancer, and neurodegenerative diseases, and as such, it is an essential target in medicine and cosmetics. Known tyrosinase inhibitors possess adverse side effects, and there are no safety regulations; therefore, it is necessary to develop new inhibitors with fewer side effects and less toxicity. Peptides are exquisitely specific to their in vivo targets, with high potencies and relatively few off-target side effects. Thus, we systematically and comprehensively investigated the tyrosinase-inhibitory abilities of N- and C-terminal cysteine/tyrosine-containing tetrapeptides by constructing a phage-display random tetrapeptide library and conducting computational molecular docking studies on novel tyrosinase tetrapeptide inhibitors. We found that N-terminal cysteine-containing tetrapeptides exhibited the most potent tyrosinase-inhibitory abilities. The positional preference of cysteine residues at the N terminus in the tetrapeptides significantly contributed to their tyrosinase-inhibitory function. The sulfur atom in cysteine moieties of N- and C-terminal cysteine-containing tetrapeptides coordinated with copper ions, which then tightly blocked substrate-binding sites. N- and C-terminal tyrosine-containing tetrapeptides functioned as competitive inhibitors against mushroom tyrosinase by using the phenol ring of tyrosine to stack with the imidazole ring of His263, thus competing for the substrate-binding site. The N-terminal cysteine-containing tetrapeptide CRVI exhibited the strongest tyrosinase-inhibitory potency (with an IC50 of 2.7 ± 0.5 μM), which was superior to those of the known tyrosinase inhibitors (arbutin and kojic acid) and outperformed kojic acid–tripeptides, mimosine-FFY, and short-sequence oligopeptides at inhibiting mushroom tyrosinase.
Matchings Meeting Quotas and Their Impact on the Blow-Up Lemma

A bipartite graph G = (U,V;E) is called $\epsilon$-regular if the edge density of every sufficiently large induced subgraph differs from the edge density of G by no more than $\epsilon$. If, in addition, the degree of each vertex in G is between $(d-\epsilon)n$ and $(d+\epsilon)n$, where d is the edge density of G and |U|=|V|=n, then G is called super $(d,\epsilon)$-regular. In [Combinatorica, 19 (1999), pp. 437--452] it was shown that if $S \subset U$ and $T \subset V$ are subsets of vertices in a super-regular bipartite graph G = (U,V;E), and if a perfect matching M of G is chosen randomly, then the number of edges of M that go between the sets S and T is roughly |S||T|/n. In this paper, we derandomize this result using the Erdos--Selfridge method of conditional probabilities. As an application, we give an alternative constructive proof of the blow-up lemma of $\komlos$, $\sarkozy$, and $\szemeredi$ (see [Combinatorica, 17 (1997), pp. 109--123] and [Random Structures Algorithms, 12 (1998), pp. 297--312]).
Positive Development in Children and the Precursors of Healthy Life-Styles: The Role of Eating Regularity and Level of Leisure Activity

The two sides of children positive development, that is physical and psychological health, have been most often investigated separately. We explored the relationships between not being overweight, respecting relational rules, regularity of eating behavior (eating breakfast) and involvement in active (e.g. playing in team sport) or sedentary (e.g. playing at videogames) leisure activities shared with friends. The study was conducted among 272 Italian children (52% female; M age = 6.85 yrs) using a multi-informant design (children, parents and teachers of physical activity). Hierarchical regression analyses revealed that regularity of eating breakfast (informed by parents) was associated to lower levels of Body Mass Index (BMI) values (objectively measured) in girls. Involvement in sedentary leisure activity with friends (informed by children) was negatively associated with respecting relational rules (evaluated by teachers of physical activity) in boys. Thus, more or less active leisure activity and more or less healthy eating behaviour have some potential relevance for present and future general adjustment of boys and girls, and not only for their physical condition. Implications for educational interventions are discussed.
Using wavelet transform self-similarity for effective multiple description video coding

Video streaming over unreliable networks requires preventive measures to avoid quality deterioration in the presence of packet losses. However, these measures result in redundancy in the transmitted data which is utilized to estimate the missing packets lost in the delivered portions. In this paper, we have used the self-similarity property if the discrete wavelet transform (DWT) to minimize the redundancy and improve the fidelity of the delivered video streams in presence of data loss. Our proposed method decomposes the video into multiple descriptions after applying the DWT. The descriptions are organized in such a way that when one of them is lost during transmission, it is estimated using the delivered portions by means of self-similarity between the DWT coefficients. In our experiments, we compare video reconstruction in the presence of data loss in one or two descriptions. Based on the experimental results, we have ascertained that our estimation method for missing coefficients by means of self-similarity is able to improve the video quality by 2.14dB and 7.26dB in case of one description and two descriptions, respectively. Moreover, our proposed method outperforms the state-of-the-art Forward Error Correction (FEC) method in case of higher bit-rates.
Self-Paced Learning: An Implicit Regularization Perspective

Self-paced learning (SPL) mimics the cognitive mechanism of humans and animals that gradually learns from easy to hard samples. One key issue in SPL is to obtain better weighting strategy that is determined by the minimizer function. Existing methods usually pursue this by artificially designing the explicit form of SPL regularizer. In this paper, we study a group of new regularizer (named self-paced implicit regularizer) that is deduced from robust loss function. Based on the convex conjugacy theory, the minimizer function for self-paced implicit regularizer can be directly learned from the latent loss function, while the analytic form of the regularizer can be even unknown. A general framework (named SPL-IR) for SPL is developed accordingly. We demonstrate that the learning procedure of SPL-IR is associated with latent robust loss functions, thus can provide some theoretical insights for its working mechanism. We further analyze the relation between SPL-IR and half-quadratic optimization and provide a group of self-paced implicit regularizer. Finally, we implement SPL-IR to both supervised and unsupervised tasks, and experimental results corroborate our ideas and demonstrate the correctness and effectiveness of implicit regularizers.
Stress processing in Mandarin and Korean second language learners of English*

This study examined stress processing among Mandarin and Korean second language learners of English and English monolinguals. While both English and Mandarin have contrastive stress at the word-level, Korean does not. Consequently, Mandarin speakers may have an advantage over Korean speakers in English stress processing, even when matched for their general English proficiency. Experiment 1 assessed participants’ stress encoding ability for nonwords in a short-term memory task. Experiment 2 examined the effect of stress in online word recognition in a lexical decision task by manipulating word frequency, stress location, and vowel quality. The results of both experiments support an advantage for English and Mandarin speakers over Korean speakers in stress processing of real words and nonwords. Only Korean speakers’ lexical judgment of nonwords was modulated by word frequency, suggesting that they do not utilize stress in lexical access. Only English speakers’ word recognition was facilitated by vowel quality changes. These results suggest that the abilities of non-native speakers to process stress in their L2 is influenced by the characteristics of the stress systems in their L1.
Association between race history and risk of superficial digital flexor tendon injury in Thoroughbred racehorses.

OBJECTIVE To determine whether race history, including the number of races and total race distance, was associated with risk of superficial digital flexor tendon (SDFT) injury in Thoroughbred racehorses in Japan. DESIGN Matched case-control study. ANIMALS 515 Thoroughbred racehorses (case horses) that sustained an SDFT injury during training or racing in Japan during 2002 and 951 horses (control horses) without SDFT injury that were matched with case horses on the basis of age and month of the latest race. PROCEDURE Variables related to race history were compared between case and control horses by means of conditional logistic regression. RESULTS The odds of SDFT injury increased as mean race distance and mean body weight at race time increased. Compared with females that had never competed in steeplechase races, males regardless of steeplechase race history and females that had competed in steeplechase races had higher odds of SDFT injury. CONCLUSIONS AND CLINICAL RELEVANCE Results suggest that longer mean distance per race, heavier mean body weight at race time, steeplechase experience, and sex (male) increased the risk of SDFT injury in Thoroughbred racehorses.
Professional learning through a generative approach to mentoring: lessons from a Training School partnership and their wider implications

This article explores the development of a generative, research‐based approach to mentoring initial teacher training students in a Training School/university partnership. Drawing on data from mentors, trainees and pupils it describes two phases of development, both of which use video recordings of participants' classroom practice to stimulate reflective dialogue. The authors point to the additional pedagogical insights made available through accessing pupil voice and the potential contribution such learning conversations can make to transforming the professional knowledge of both mentors and trainees. They highlight the dispositions and conditions which support the co‐construction of this inclusive approach and how it has contributed to the development of the school as a learning community. The authors suggest its wider relevance and how it can contribute to the creation by the profession of a new epistemological base for professional learning.