Miracle-dz/UniFAR-FTUs huggingface dataset:
Associations of Mitochondrial Haplogroups B4 and E with Biliary Atresia and Differential Susceptibility to Hydrophobic Bile Acid

Mitochondrial dysfunction has been implicated in the pathogenesis of biliary atresia (BA). This study aimed to determine whether a specific mitochondrial DNA haplogroup is implicated in the pathogenesis and prognosis of BA. We determined 40 mitochondrial single nucleotide polymorphisms in 15 major mitochondrial haplogroups by the use of 24-plex PCR and fluorescent beads combined with sequence-specific oligonucleotide probes in 71 patients with BA and in 200 controls in the Taiwanese population of ethnic Chinese background. The haplogroup B4 and E prevalence were significantly lower and higher respectively, in the patients with BA than in the controls (odds ratios, 0.82 [p = 0.007] and 7.36 [p = 0.032] respectively) in multivariate logistic-regression analysis. The 3-year survival rate with native liver was significantly lower in haplogroup E than the other haplogroups (P = 0.037). A cytoplasmic hybrid (cybrid) was obtained from human 143B osteosarcoma cells devoid of mtDNA (ρ0 cell) and was fused with specific mtDNA bearing E and B4 haplogroups donated by healthy Taiwanese subjects. Chenodeoxycholic acid treatment resulted in significantly lower free radical production, higher mitochondrial membrane potential, more viable cells, and fewer apoptotic cybrid B4 cells than parental 143B and cybrid E cells. Bile acid treatment resulted in a significantly greater protective mitochondrial reaction with significantly higher mitochondrial DNA copy number and mitofusin 1 and 2 concentrations in cybrid B4 and parental cells than in cybrid E cells. The results of the study suggested that the specific mitochondrial DNA haplogroups B4 and E were not only associated with lower and higher prevalence of BA respectively, in the study population, but also with differential susceptibility to hydrophobic bile acid in the cybrid harboring different haplogroups.
Food Preferences Communicated via Symbol Discrimination by a California Sea Lion (Zalophus californianus)

This study investigates the food preferences of a single California sea lion, Zalophus californianus. Through operant conditioning the sea lion was taught to associate arbitrary, abstract symbols with different food types. The symbols were then used in paired comparisons to permit the sea lion to indicate and obtain its preferred food. Results indicated a preference for foods that are high in nutritional value and low in moisture. Knowledge of food preferences gained in this manner may be useful in improving the reinforcement process, providing environmental enrichment, and enhancing animal-human communication.
Forming a Professional Counselor Identity: The Impact of Identity Processing Style

This study examined the impact of identity processing style on professional counselor identity development. 136 masters students in a CACREP-accredited counseling program completed a survey with measures of counselor identity and identity style. Results of the study signify that differences in identity processing style have an impact on the development of a professional counselor identity. The use of both informational and normative processing styles appear beneficial in forming a professional counselor identity, though the informational style alone was indicative of a professional counselor identity beyond identity commitment. The diffuse/avoidant style seems least suitable for developing a professional counselor identity.
3 Automating the Generation of a Wide-coverage LFG for French using a MetaGrammar

In this paper, we explain how the notion of MetaGrammar, which has successfully been used for generating wide-coverage tree adjoining grammars (TAGs) for various languages such as French (Abeillé et al. (1999)) and German (Gerdes (2002)), may be used to generate a wide-coverage Lexical Functional Grammar (LFG) for French. We first introduce the notion of MetaGrammar and present the tools we use to automatically generate, from a compact MetaGrammar hierarchy, a LFG for French: the grammar writer specifies in compact manner syntactic properties that are usually encoded separately in the LFG machinery in the lexicon, in lexical rules and in rewriting rules. From this hierarchy an LFG is automatically generated. We also propose an augmentation of the existing MetaGrammar tool.
Associations of lipid levels during gestation with hypertensive disorders of pregnancy and gestational diabetes mellitus: a prospective longitudinal cohort study

Objective To assess associations of elevated lipid levels during gestation with hypertensive disorders of pregnancy (HDP) and gestational diabetes mellitus (GDM). Methods This prospective cohort study was conducted in a tertiary maternal hospital in Shanghai, China from February to November 2014. Lipid constituents, including triglycerides (TGs), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-c) and high-density lipoprotein cholesterol (HDL-c) of 1310 eligible women were assessed in the first (10–13+ weeks), second (22–28 weeks) and third (30–35 weeks) trimesters consecutively. Associations of lipid profiles with HDP and/or GDM outcomes were assessed. Results Compared with the normal group, maternal TG concentrations were higher in the HDP/GDM groups across the three trimesters (p<0.001); TC and LDL-c amounts were only higher in the first trimester for the HDP and GDM groups (p<0.05). HDL-c levels were similar in the three groups. Compared with intermediate TG levels (25–75th centile), higher TG amounts (>75th centile) were associated with increased risk of HDP/GDM in each trimester with aORs (95% CI) of 2.04 (1.41 to 2.95), 1.81 (1.25 to 2.63) and 1.78 (1.24 to 2.54), respectively. High TG elevation from the first to third trimesters (>75th centile) was associated with increased risk of HDP, with an aOR of 2.09 (1.16 to 3.78). High TG elevation before 28 weeks was associated with increased risk of GDM, with an aOR of 1.67 (1.10 to 2.54). TG elevation was positively correlated with weight gain during gestation (R=0.089, p=0.005). Conclusions Controlling weight gain during pregnancy could decrease TG elevation and reduce the risk of HDP/GDM. TGs could be used as follow-up parameters during complicated pregnancy, while other lipids are meaningful only in the first trimester.
Supervised and Unsupervised Sound Retrieval by Vocal Imitation

Searching sounds with text labels is often problematic and time consuming as text labels do not often describe the detailed audio content. Query by example is a way to improve the effectiveness and efficiency of sound retrieval. In this paper we propose a novel approach for sound query by example: query by vocal imitation. Vocal imitation is commonly used in human communication and can be employed for novel human-computer interaction. We propose two related systems. The supervised system addresses the retrieval problem by vocal imitation recognition. It trains a multi-class classifier using training vocal imitations of different sound classes in the library and classifies a new imitation query into one of the classes. This system thus cannot retrieve sounds that are not trained. The unsupervised system is more flexible in that it measures the feature distance between the imitation query and each sound in the library and returns sounds the most similar to the query. One challenge of designing these systems is finding an effective feature representation of imitation queries and sounds in the library. Existing handcrafted audio features may not work well given the variety of vocal imitations and the mismatch between vocal imitations and actual sounds. We propose to learn feature representations from training vocal imitations automatically using a Stacked Auto-Encoder (SAE). Experiments show that sound retrieving performance by automatically learned features outperform those carefully handcrafted ones that were used in existing systems in both supervised and unsupervised settings.
Periconceptional Folate Deficiency and Implications in Neural Tube Defects

Nutritional deficiencies are preventable etiological and epigenetic factors causing congenital abnormalities, first cause of infant mortality. Folate deficiency has a well-established teratogenic effect, leading to an increasing risk of neural tube defects. This paper highlights the most recent medical literature about folate deficiency, be it maternal or paternal. It then focuses on associated deficiencies as nutritional deficiencies are multiple and interrelated. Observational and interventional studies have all been consistent with a 50–70% protective effect of adequate women consumption of folates on neural tube defects. Since strategies to modify women's dietary habits and vitamin use have achieved little progress, scientific as well as political effort is mandatory in order to implement global preventive public health strategies aimed at improving the alimentation of women in reproductive age, especially folic acid supplementation. Even with the recent breakthrough of fetal surgery for myelomeningocele, the emphasis should still be on prevention as the best practice rather than treatment of neural tube defects.
Extended X‐ray emission from the BL Lac object PKS 0521‐365

Models that seek to unify BL Lacs and low-power radio galaxies predict that the two types of object should show similar isotropically emitted X-ray emission. Testing this is usually limited by difficulties in separating strong X-ray emission from a BL Lac nucleus and surrounding low-surface brightness emission. In this paper we report ROSAT HRI observations of the z = 0.055 BL Lac object PKS 0521 365. We are able to separate a luminous extended X-ray component from the bright nucleus. Using a new radio map, we show that it is unlikely that the extended emission is due to inverseCompton scattering of photons from the active nucleus, and instead interpret it as thermal emission from dense, rapidly cooling gas. This is a more extreme environment than is found in typical FRI radio galaxies, and may pose a problem for unified models.
Effects of levomilnacipran ER on fatigue symptoms associated with major depressive disorder

The aim of this study was to evaluate the effects of levomilnacipran extended-release (ER) on depression-related fatigue in adults with major depressive disorder. Post-hoc analyses of five phase III trials were carried out, with evaluation of fatigue symptoms based on score changes in four items: Montgomery–Åsberg Depression Rating Scale (MADRS) item 7 (lassitude), and 17-item Hamilton Depression Rating Scale (HAMD17) items 7 (work/activities), 8 (retardation), and 13 (somatic symptoms). Symptom remission was analyzed on the basis of score shifts from baseline to end of treatment: MADRS item 7 and HAMD17 item 7 (from ≥2 to ⩽1); HAMD17 items 8 and 13 (from ≥1 to 0). The mean change in MADRS total score was analyzed in patients with low and high fatigue (MADRS item 7 baseline score <4 and ≥4, respectively). Patients receiving levomilnacipran ER had significantly greater mean improvements and symptom remission (no/minimal residual fatigue) on all fatigue-related items: lassitude (35 vs. 28%), work/activities (43 vs. 35%), retardation (46 vs. 39%), somatic symptoms (26 vs. 18%; all Ps<0.01 versus placebo). The mean change in MADRS total score was significantly greater with levomilnacipran ER versus placebo in both low (least squares mean difference=−2.8, P=0.0018) and high (least squares mean difference=−3.1, P<0.0001) fatigue subgroups. Levomilnacipran ER treatment was effective in reducing depression-related fatigue in adult patients with major depressive disorder and was associated with remission of fatigue symptoms.
Second language learners' processing of inflected words: Behavioral and ERP evidence for storage and decomposition

This study reports the results of two behavioral and two event-related brain potential (ERP) experiments examining the processing of inflected words in advanced second language (L2) learners with Russian as their native language (L1) who learnt German as an L2 after childhood. Two different subsystems of German inflection were studied, participial inflection and noun plurals. For participial forms, L2 learners were found to widely generalize the -t suffixation rule in a nonce-word elicitation task, and in the ERP experiment they showed an anterior negativity followed by a P600 – both results resembling previous findings from native speakers of German on the same materials. For plural formation, the L2 learners displayed different preference patterns for regular and irregular forms in an off-line plural judgment task. Regular and irregular plural forms also differed clearly with regard to their brain responses. Whereas -s plural regularizations produced a P600 component, irregularizations elicited an N400. In contrast to native speakers of German, however, the L2 learners did not show an anterior negativity for -s plural regularizations. Taken together, the results show clear dissociations between regular and irregular inflection for both morphological subsystems. We argue that the two processing routes posited by dual-mechanism models of inflection (lexical storage and morphological decomposition) are also employed by L2 learners, even though the decomposition route appears to be more limited in the L2 learners than in the native controls.
Globus Pallidus Externus Neurons Expressing parvalbumin Interconnect the Subthalamic Nucleus and Striatal Interneurons

The globus pallidus externus (GP) is a nucleus of the basal ganglia (BG), containing GABAergic projection neurons that arborize widely throughout the BG, thalamus and cortex. Ongoing work seeks to map axonal projection patterns from GP cell types, as defined by their electrophysiological and molecular properties. Here we use transgenic mice and recombinant viruses to characterize parvalbumin expressing (PV+) GP neurons within the BG circuit. We confirm that PV+ neurons 1) make up ~40% of the GP neurons 2) exhibit fast-firing spontaneous activity and 3) provide the major axonal arborization to the STN and substantia nigra reticulata/compacta (SNr/c). PV+ neurons also innervate the striatum. Retrograde labeling identifies ~17% of pallidostriatal neurons as PV+, at least a subset of which also innervate the STN and SNr. Optogenetic experiments in acute brain slices demonstrate that the PV+ pallidostriatal axons make potent inhibitory synapses on low threshold spiking (LTS) and fast-spiking interneurons (FS) in the striatum, but rarely on spiny projection neurons (SPNs). Thus PV+ GP neurons are synaptically positioned to directly coordinate activity between BG input nuclei, the striatum and STN, and thalamic-output from the SNr.
Comprehensive Immunolocalization Studies of a Putative Serotonin Receptor from the Alimentary Canal of Aedes aegypti Larvae Suggest Its Diverse Roles in Digestion and Homeostasis

Serotonin regulates key processes including digestion and homeostasis in insects. Serotonin effects are mediated by serotonin receptors that transduce information through initiation of second messenger signaling pathways. Lack of information on serotonin receptors associated with the alimentary canal impedes the understanding of the serotonergic role in insect physiology. To address this void, the present study has cloned and identified a putative serotonin receptor (hereafter AaSeR-1) from the alimentary canal of Aedes aegypti (yellow fever mosquito) larvae. In addition to in-silico analyses of AaSeR-1 primary sequence, immunohistochemical investigations were carried out to elucidate receptor expression patterns. Specific AaSeR-1 immunofluorescence was detected in the caeca, the mid- and hindgut, including the Malpighian tubules. These findings point out not only receptor ubiquitous nature but also its involvement in regulation of different stages of nutrient processing and homeostasis. Furthermore, AaSeR-1 may mediate an array of effects through its differential expression at various cell compartments. While AaSeR-1 specific immunofluorescence was depicted in the nucleus and nucleolus of principal cells of the anterior midgut, in the posterior, analyses suggest receptor association with the plasma membrane of both principal and regenerative cells. In addition, AaSeR-1 immunofluorescence was also found in some enteroendocrine cells and in both circular and longitudinal muscles that innervate the alimentary canal. Overall, immunohistochemical analyses of AaSeR-1 expression indicate that this receptor exercises multiple roles in digestion- and homeostasis-related mechanisms.
The axonal arborizations of lateral geniculate neurons in the striate cortex of the cat

Horseradish peroxidase (HRP) was injected into the optic radiations of adult cats. With placements close to the lateral geniculate nucleus (LGN), the enzyme diffused retrogradely along the axons of geniculocortical relay neurons, entered their cell bodies, and, after reaction with diaminobenzidine, produced a Golgi‐like staining of entire neurons. When the injections were made close to the visual cortex, the enzyme diffused anterogradely and filled complete axonal arborizations in area 17.
Asynchronous Parallel Empirical Variance Guided Algorithms for the Thresholding Bandit Problem

This paper considers the multi-armed thresholding bandit problem -- identifying all arms whose expected rewards are above a predefined threshold via as few pulls (or rounds) as possible -- proposed by Locatelli et al. [2016] recently. Although the proposed algorithm in Locatelli et al. [2016] achieves the optimal round complexity in a certain sense, there still remain unsolved issues. This paper proposes an asynchronous parallel thresholding algorithm and its parameter-free version to improve the efficiency and the applicability. On one hand, the proposed two algorithms use the empirical variance to guide the pull decision at each round, and significantly improve the round complexity of the "optimal" algorithm when all arms have bounded high order moments. The proposed algorithms can be proven to be optimal. On the other hand, most bandit algorithms assume that the reward can be observed immediately after the pull or the next decision would not be made before all rewards are observed. Our proposed asynchronous parallel algorithms allow making the choice of the next pull with unobserved rewards from earlier pulls, which avoids such an unrealistic assumption and significantly improves the identification process. Our theoretical analysis justifies the effectiveness and the efficiency of proposed asynchronous parallel algorithms.
Towards Data Intensive Many-Task Computing

Many-task computing aims to bridge the gap between two computing paradigms, high throughput computing and high performance computing. Many task computing denotes high-performance computations comprising multiple distinct activities, coupled via file system operations. The aggregate number of tasks, quantity of computing, and volumes of data may be extremely large. Traditional techniques to support many-task computing commonly found in scientific computing (i.e. the reliance on parallel file systems with static configurations) do not scale to today’s largest systems for data intensive application, as the rate of increase in the number of processors per system is outgrowing the rate of performance increase of parallel file systems. We argue that in such circumstances, data locality is critical to the successful and efficient use of large distributed systems for data-intensive applications. We propose a “data diffusion” approach to enable dataintensive many-task computing. Data diffusion acquires compute and storage resources dynamically, replicates data in response to demand, and schedules computations close to data, effectively harnessing data locality in application data access patterns. As demand increases, more resources are acquired, thus allowing faster response to subsequent requests that refer to the same data; when demand drops, resources are released. To explore the feasibility of data diffusion, we offer both a theoretical and empirical analysis. We define an abstract model for data diffusion, define and implement scheduling policies with heuristics that optimize real world performance, and develop a competitive online caching eviction policy. We also offer many empirical experiments to explore the benefits of data diffusion, both under static and dynamic resource provisioning. We show performance improvements of one to two orders of magnitude across three diverse workloads when compared to the performance of parallel file systems with throughputs approaching 80Gb/s on a modest cluster of 200 processors. We also compare data diffusion with a best model for active storage, contrasting the difference between a pull-model found in data diffusion and a push-model found in active storage, on up to 5832 processors. We conclude the chapter with performance results from a large scale astronomy application demonstrating that our approach improves both its performance and scalability.
Explaining Memory Amplification: Is It All About the Test Format?

Trauma-exposed people commonly exhibit a “memory amplification” effect, endorsing exposure to more traumatic events over time. Studies reporting this phenomenon have typically relied on checklists, where participants read event descriptions and indicate (yes/no) their exposure. We examined whether that approach is vulnerable to response biases and memory errors. In two experiments, participants viewed negative photos and completed an Old-New recognition test. In Experiment 1, participants completed either a photo recognition test or description test—composed of written descriptions of negative photos. In Experiment 2, we measured analogue PTSD symptoms and participants completed the description test twice, 24 hr apart. Those in the description test condition performed worse on the memory test and were more biased to endorse negative photos compared with the photo test condition. Furthermore, this bias to endorse negative photos increased over time and was related to analogue PTSD symptoms. Overall, our findings suggest that test format plays a role in memory amplification.
Heterogeneity and Cyclical Unemployment

We model worker heterogeneity in the rents from being employed in a Diamond-Mortensen-Pissarides model of matching and unemployment. We show that heterogeneity, reflecting differences in match quality and worker assets, reduces the extent of fluctuations in separations and unemployment. We find that the model faces a trade-off--it cannot produce both realistic dispersion in wage growth across workers and realistic cyclical fluctuations in unemployment.