Miracle-dz/UniFAR-FTUs huggingface dataset:
Integration of Metabolomic and Proteomic Phenotypes

Statistical mining and integration of complex molecular data including metabolites, proteins, and transcripts is one of the critical goals of systems biology (Ideker, T., Galitski, T., and Hood, L. (2001) A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2, 343–372). A number of studies have demonstrated the parallel analysis of metabolites and large scale transcript expression. Protein analysis has been ignored in these studies, although a clear correlation between transcript and protein levels is shown only in rare cases, necessitating that actual protein levels have to be determined for protein function analysis. Here, we present an approach to investigate the combined covariance structure of metabolite and protein dynamics in a systemic response to abiotic temperature stress in Arabidopsis thaliana wild-type and a corresponding starch-deficient mutant (phosphoglucomutase-deficient). Independent component analysis revealed phenotype classification resolving genotype-dependent response effects to temperature treatment and genotype-independent general temperature compensation mechanisms. An observation is the stress-induced increase of raffinose-family-oligosaccharide levels in the absence of transitory starch storage/mobilization in temperature-treated phosphoglucomutase plants indicating that sucrose synthesis and storage in these mutant plants is sufficient to bypass the typical starch storage/mobilization pathways under abiotic stress. Eventually, sample pattern recognition and correlation network topology analysis allowed for the detection of specific metabolite-protein co-regulation and assignment of a circadian output regulated RNA-binding protein to these processes. The whole concept of high-dimensional profiling data integration from many replicates, subsequent multivariate statistics for dimensionality reduction, and covariance structure analysis is proposed to be a major strategy for revealing central responses of the biological system under study.
Victimization from Peer Aggression and/or Bullying: Prevalence, Overlap, and Psychosocial Characteristics

ABSTRACT Bullying and peer victimization are overlapping concepts related to aggressive behaviors by peers, prevalent among children and adolescents worldwide. Bullying has been suggested to be particularly harmful for the victim, yet few studies have empirically explored the differences between peer victimization and victimization from bullying. In the present study, a multinomial approach was applied to examine the prevalence and psychosocial profiles of teenagers that reported frequent peer victimization and/or episodes of being bullied, in a sample of 3,447 Finnish middle school students (1,757 girls and 1,690 boys; mean age 14.3 years). Convergent, multi-identified victims were found to be most likely to show high levels of depressive symptoms, but all categories of victims showed increased levels of depressive symptoms compared to non-victims. Notably, victims of bullying and victims of peer aggression differed in terms of aggressive behavior and perceived peer support. The results are discussed in terms of victim identity and identification.
Thresholding Word Activations for Response Scoring - Modelling Psycholinguistic Data

In the present paper we replicate simulations of infant word learning and the effect of variation in the input. We then investigate to what extent the results are inﬂuenced by the way in which the continuous response functions are treated and what effects the use of thresholds can have on the data. Our results show that the underlying response pattern, as uncovered by different thresholds, varies greatly. Nonetheless, the overall output of the model is often correct and able to generalise to unseen data. Thus, we show that the model can give correct responses even in uncertain circumstances. Links of this ﬁnding to language acquisition research are discussed.
Tardis 2.0: An Optimized Time Traveling Coherence Protocol

The scalability of cache coherence protocols is a significant challenge in multicore and other distributed shared memory systems. Traditional snoopy and directory-based coherence protocols are difficult to scale up to many-core systems because of the overhead of broadcasting and storing sharers for each cacheline. Tardis, a recently proposed coherence protocol, shows potential in solving the scalability problem, since it only requires O(logN) storage per cacheline for an N-core system and needs no broadcasting support. The original Tardis protocol, however, only supports the sequential consistency memory model. This limits its applicability in real systems since most processors today implement relaxed consistency models like Total Store Order (TSO). Tardis also incurs large network traffic overhead on some benchmarks due to an excessive number of renew messages. Furthermore, the original Tardis protocol has suboptimal performance when the program uses spinning to communicate between threads. In this paper, we address these downsides of Tardis protocol and make it significantly more practical. Specifically, we discuss the architectural, memory system and protocol changes required in order to implement TSO consistency model on Tardis, and prove that the modified protocol satisfies TSO. We also propose optimizations for better leasing policies and to handle program spinning. Evaluated on 20 benchmarks, optimized Tardis at 64 (256) cores can achieve average performance improvement of 15.8% (8.4%) compared to the baseline Tardis and 1% (3.4%) compared to the baseline directory protocol. Our optimizations also reduce the average network traffic by 4.3% (6.1%) compared to the baseline directory protocol. On this set of benchmarks, optimized Tardis improves on a fullmap directory protocol in the metrics of energy, performance and storage, while being simpler to implement.
A Derivative-Based Approach for QT-Segment Feature Extraction in Digitized ECG Record

Automatic electrocardiogram analysis using different signal processing technique is one of the prominent areas of research in biomedical engineering. This paper illustrates a simple approach for time plane feature extraction in the QT segment. At first, the R peaks are accurately determined using a simple derivative-based approach and hence heart rate is calculated. Next, the baseline points of all cardiac cycles in the dataset are determined in the TP segment and the baseline modulation in the signal is eliminated by an empirical formula. Finally, the characteristic points Q, Q-offset, S, S-offset, T-onset, T and T-offset are calculated for all cycles using a magnitude and slope threshold based method. Hence, QRS width, ST segment, QT segment and (QT)c are determined. ECG data for 30 second interval from MIT-PTB diagnostic database is used for testing the algorithm.
Medial Medullary Infarction: Clinical, Imaging, and Outcome Study in 86 Consecutive Patients

Background and Purpose— Clinical-imaging correlation and long-term clinical outcomes remain to be investigated in medial medullary infarction (MMI). Methods— We studied clinical, MRI, and angiographic data of 86 consecutive MMI patients. The lesions were correlated with clinical findings, and long-term outcomes, divided into mild and severe (modified Rankin scale >3), were assessed by telephone interview. Central poststroke pain (CPSP) was defined as persistent pain with visual numeric scale ≥4. Results— The lesions were located mostly in the rostral medulla (rostral 76%, rostral+middle 16%), while ventro-dorsal lesion patterns include ventral (V, 20%), ventral+middle (VM, 33%), and ventral+middle+dorsal (VMD, 41%). Clinical manifestations included motor dysfunction in 78 patients (91%), sensory dysfunction in 59 (73%), and vertigo/dizziness in 51 (59%), each closely related to involvement of ventral, middle, and dorsal portions, respectively (P<0.001, each). Vertebral artery (VA) atherosclerotic disease relevant to the infarction occurred in 53 (62%) patients, mostly producing atheromatous branch occlusion (ABO). Small vessel disease (SVD) occurred in 24 (28%) patients. ABO was more closely related to VMD (versus V+VM) than was SVD (P=0.035). During follow-up (mean 71 months), 11 patients died, and recurrent strokes occurred in 11. Old age (P=0.001) and severe motor dysfunction at admission (P=0.001) were factors predicting poor prognosis. CPSP, occurring in 21 patients, was closely (P=0.013) related to poor clinical outcome. Conclusion— MMI usually presents with a rostral medullary lesion, with a good clinical ventro-dorsal imaging correlation, caused most frequently by ABO followed by SVD. A significant proportion of patients remain dependent or have CPSP.
On the circum(sub)stellar environment of brown dwarfs in Taurus

Aims. We want to investigate whether brown dwarfs (BDs) form like stars or are ejected embryos. We study the presence of disks around BDs in the Taurus cloud, and discuss implications for substellar formation models. Methods. We use photometric measurements from the visible to the far infrared to determine the spectral energy distributions (SEDs) of Taurus BDs. Results. We use Spitzer color indices, Hα as an accretion indicator, and models fit to the SEDs in order to estimate physical parameters of the disks around these BDs. We study the spatial distribution of BDs with and without disks across the Taurus aggregates, and we find that BDs with and without disks are not distributed regularly across the Taurus cloud. Conclusions. We find that 48%±14% of Taurus BDs have a circumstellar disk signature, a ratio similar to recent results from previous authors in other regions. We fit the SEDs and find that none of the disks around BDs in Taurus can be fitted convincingly with a flaring index β = 0, indicating that heating by the central object is efficient and that the disks we observe retain a significant amount of gas. We find that BDs with disks are proportionally more numerous in the northern Taurus filament, possibly the youngest filament. We do not find such a clear segregation for classical T Tauri stars (CTTS) and weak-lined T Tauri stars (WTTS), suggesting that, in addition to the effects of evolution, any segregation effects could be related to the mass of the object. A by-product of our study is to propose a recalibration of the Barrado y Navascues & Martin (2003) accretion limit in the substellar domain. The global shape of the limit fits our data points if it is raised by a factor 1.25–1.30.
PERIL AND PLEASURE: AN RDOC‐INSPIRED EXAMINATION OF THREAT RESPONSES AND REWARD PROCESSING IN ANXIETY AND DEPRESSION

As a step toward addressing limitations in the current psychiatric diagnostic system, the National Institute of Mental Health recently developed the Research Domain Criteria (RDoC) to stimulate integrative research—spanning self‐report, behavior, neural circuitry, and molecular/genetic mechanisms—on core psychological processes implicated in mental illness. Here, we use the RDoC conceptualization to review research on threat responses, reward processing, and their interaction. The first section of the manuscript highlights the pivotal role of exaggerated threat responses—mediated by circuits connecting the frontal cortex, amygdala, and midbrain—in anxiety, and reviews data indicating that genotypic variation in the serotonin system is associated with hyperactivity in this circuitry, which elevates the risk for anxiety and mood disorders. In the second section, we describe mounting evidence linking anhedonic behavior to deficits in psychological functions that rely heavily on dopamine signaling, especially cost/benefit decision making and reward learning. The third section covers recent studies that document negative effects of acute threats and chronic stress on reward responses in humans. The mechanisms underlying such effects are unclear, but the fourth section reviews new optogenetic data in rodents indicating that GABAergic inhibition of midbrain dopamine neurons, driven by activation of the habenula, may play a fundamental role in stress‐induced anhedonia. In addition to its basic scientific value, a better understanding of interactions between the neural systems that mediate threat and reward responses may offer relief from the burdensome condition of anxious depression.
What Is the Accretion Rate in NGC 4258?

We estimate the accretion rate Ṁ onto the black hole in the nucleus of NGC 4258. The result is model dependent. We find that a thin disk that is flat out to ≳2 × 103GM/c2 (M≡black hole mass) and that has inclination equal to that of the masing disk must have Ṁ ≃ 0.01 M☉ yr-1 for consistency with near-infrared data. A thin disk that is warped at ~103GM/c2 requires Ṁ ≳ 1.5 × 10-4 M☉ yr-1 for consistency with near-infrared data. Reasonable warp models and the near-infrared data are not consistent with Ṁ as low as the 7 × 10-5α M☉ yr-1 proposed by Neufeld & Maloney. An advection-dominated flow model combined with the X-ray data implies Ṁ ≃ 0.01 M☉ yr-1. Consistency with a tight 22 GHz upper limit on the flux from the central source requires a transition radius of ~(10-100)GM/c2, although the 22 GHz upper limit may be relaxed by appeal to free-free absorption. Physical conditions in the observed VLBI jet features can also be related to conditions in the inner accretion flow. We conclude with a list of observations that might further constrain Ṁ.
Efficient XML storage based on DTM for read-oriented workloads

We propose an XML storage scheme based on Document Table Model (DTM) which expresses an XML document as a table form. When performing query processing on large scale XML data, XML storage schemes on secondary storage and their access methods greatly affect the entire performance. For this reason, we developed an XQuery processing scheme in which an XML document is internally represented as a set of DTM blocks and can be directly stored on secondary storage. Our scheme is tailored for read-oriented workloads, and an XML document is stored on disks as arrays of nodes. We analyzed the actual data access patterns to DTM appeared in processing XML queries, and employed the combination of informed prefetching and scan-resistant buffer management based on the analysis. Our experimental results showed that our storage scheme outperforms competing schemes with respect to I/O-intensive workloads, and our sophisticated prefetching and caching increase overall throughput without significant drawbacks.
Does managerial involvement in workplace coaching impact the outcome? A mixed-methods study into the current methods managers employ and the impacts on coaching effectiveness

Research into workplace-training suggests actions taken by managers, such as discussing applying the training, can significantly impact the effectiveness of training. However, little is known as to whether these findings translate to workplace-coaching. This mixed-methods study gathered information on current practices involving managers and the perceived effectiveness on the outcomes of coaching from coachees, managers and practitioners within the field. Those approaches that required discretionary effort as opposed to prescribed involvement were perceived to have a greater impact on coaching outcomes. There appeared to be no cumulative effect; more involvement did not translate to a perception of greater impact on outcomes.
Expression of the Anthracycline-Metabolizing Enzyme Carbonyl Reductase 1 in Hearts from Donors with Down Syndrome

Cancer patients with Down syndrome (DS) are susceptible to developing anthracycline-related cardiotoxicity. The pathogenesis of anthracycline-related cardiotoxicity has been linked to the intracardiac synthesis of alcohol metabolites by carbonyl reductase 1 (CBR1). CBR1 is located in the DS critical region (21q22.12). The expression of CBR1 in hearts from individuals with DS has not been characterized. This study documented CBR1 expression in hearts from donors with DS (n = 4) and donors without DS (n = 15). The DS samples showed 1.8-fold higher CBR1 mRNA levels compared to the non-DS samples (levels in DS samples were 3.3-relative fold, and those in non-DS were 1.8-relative fold; p = 0.012). CBR1 protein levels were 1.9-fold higher in DS samples than in non-DS samples (13.5 ± 7.7 versus 7.2 ± 3.9 nmol/g cytosolic protein, respectively; p = 0.029). CBR1 activity for daunorubicin was 1.7-fold higher in DS samples than in non-DS samples (3.8 ± 0.1 versus 2.3 ± 0.2 nmol daunol/min · mg, respectively; p = 0.050). CBR1 1096G>A (rs9024) affects CBR1 activity, and one heart trisomic for the variant A allele (A/A/A) exhibited low enzymatic activity. These findings suggest that increased CBR1 expression in the hearts of individuals with DS may contribute to the risk of anthracycline-related cardiotoxicity.
The Generation of Live Offspring from Vitrified Oocytes

Oocyte cryopreservation is extremely beneficial for assisted reproductive technologies, the treatment of infertility and biotechnology and offers a viable alternative to embryo freezing and ovarian grafting approaches for the generation of embryonic stem cells and live offspring. It also offers the potential to store oocytes to rescue endangered species by somatic cell nuclear transfer and for the generation of embryonic stem cells to study development in these species. We vitrified mouse oocytes using a range of concentrations of trehalose (0 to 0.3 M) and demonstrated that 0.1 and 0.3 M trehalose had similar developmental rates, which were significantly different to the 0.2 M cohort (P<0.05). As mitochondria are important for fertilisation outcome, we observed that the clustering and distribution of mitochondria of the 0.2 M cohort were more affected by vitifrication than the other groups. Nevertheless, all 3 cohorts were able to develop to blastocyst, following in vitro fertilisation, although developmental rates were better for the 0.1 and 0.3 M cohorts than the 0.2 M cohort (P<0.05). Whilst blastocysts gave rise to embryonic stem-like cells, it was apparent from immunocytochemistry and RT-PCR that these cells did not demonstrate true pluripotency and exhibited abnormal karyotypes. However, they gave rise to teratomas following injection into SCID mice and differentiated into cells of each of the germinal layers following in vitro differentiation. The transfer of 2-cell embryos from the 0.1 and 0.3 M cohorts resulted in the birth of live offspring that had normal karyotypes (9/10). When 2-cell embryos from vitrified oocytes underwent vitrification, and were thawed and transferred, live offspring were obtained that exhibited normal karyotypes, with the exception of one offspring who was larger and died at 7 months. We conclude that these studies highlight the importance of the endometrial environment for the maintenance of genetic stability and thus the propagation of specific genetic traits.
Structure, Function, and Cortical Representation of the Rat Submandibular Whisker Trident

Although the neurobiology of rodent facial whiskers has been studied intensively, little is known about sensing in other vibrissae. Here we describe the under-investigated submandibular “whisker trident” on the rat's chin. In this three-whisker array, a unique unpaired midline whisker is laterally flanked by two slightly shorter whiskers. All three whiskers point to the ground and are curved backwards. Unlike other whiskers, the trident is not located on an exposed body part. Trident vibrissae are not whisked and do not touch anything over long stretches of time. However, trident whiskers engage in sustained ground contact during head-down running while the animal is exploring or foraging. In biomechanical experiments, trident whiskers follow caudal ground movement more smoothly than facial whiskers. Remarkably, deflection angles decrease with increasing ground velocity. We identified one putative trident barrel in the left somatosensory cortex and two barrels in the right somatosensory cortex. The elongated putative trident-midline barrel is the longest and largest whisker barrel, suggesting that the midline trident whisker is of great functional significance. Cortical postsynaptic air-puff responses in the trident representation show much less temporal precision than facial whisker responses. Trident whiskers do not provide as much high-resolution information about object contacts as facial whiskers. Instead, our observations suggest an idiothetic function: their biomechanics allow trident whiskers to derive continuous measurements about ego motion from ground contacts. The midline position offers unique advantages in sensing heading direction in a laterally symmetric manner. The changes in trident deflection angle with velocity suggest that trident whiskers might function as a tactile speedometer.
Researching Rural American Schools: Continuing Cultural Themes and Cultural Conflicts in the Countryside.

The "rural school problem" continues to plague current researchers, as it did school reformers of the past. There are basically two academic literatures focusing upon rural communities and their schools where rurality rather than ethnicity is the focus. The historical literature typically features tales of rural economic decline, changing demography, and emerging industrial culture from the Civil War through the Cold War. The second perspective also deals with major social transformations in economy, location, and occupation, but deals with the international scene rather than the domestic. Both perspectives address the role of formai schooling in transforming rural populations into modern citizens. Braxton County, West Virginia, fits the rural community types of "depressed rural" and "isolated rural. " Sociologists hypothesize about the potential for rural schools to bridge the alleged chasm between rural Appalachia and the national culture. Observations in Braxton County schools suggest that instructional and extracurricular activities are intentionally compensatory, designed to offset some of the perceived cultural disadvantages of regional rurality, isolation, and poverty. However, cultural opposition to mainstream educational goals arises from a strong sense of place, the hunting subculture, the lack of role models seeking career goals, fatalist and fundamentalist beliefs, and the low valve placed on high school and higher education. (Contains 25 references.) (KS) *********************************************************************** Reproductions supplied by EDRS are the best that can be made from the original document. ***********************************************************************
The driving factors of continuance online shopping: Gender differences in behaviour the case of Saudi Arabia

This study proposes a revised technology acceptance model that integrates expectation confirmation theory to measure gender differences with regard to continuance online shopping intentions in Saudi Arabia. The 465-respondent sample consists of 68.8% women and 31.4% men. A structural equation model confirms model fit. Perceived usefulness, enjoyment, and subjective norms are determinants of online shopping continuance in Saudi Arabia. Both male and female groups are equivalent. The structural weights are also largely equivalent, but the regression paths from perceived usefulness to subjective norms and to continuous intention are not invariant between men and women. The model was operationally generalized across the whole of Saudi Arabia. This research moves beyond online shopping intentions and includes factors affecting online shopping continuance. The research model explains 65% of the intention to continue shopping online. This research suggests that online strategies cannot ignore either the direct and indirect gender differences on continuance intentions in Saudi Arabia. The model can be generalized across Saudi Arabia.