Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of porcine reproductive and respiratory syndrome (PRRS) virus structural and non-structural proteins in virus pathogenesis

Abstract Porcine reproductive and respiratory syndrome (PRRS) is an economically devastating viral disease affecting the swine industry worldwide. The etiological agent, PRRS virus (PRRSV), possesses a RNA viral genome with nine open reading frames (ORFs). The ORF1a and ORF1b replicase-associated genes encode the polyproteins pp1a and pp1ab, respectively. The pp1a is processed in nine non-structural proteins (nsps): nsp1α, nsp1β, and nsp2 to nsp8. Proteolytic cleavage of pp1ab generates products nsp9 to nsp12. The proteolytic pp1a cleavage products process and cleave pp1a and pp1ab into nsp products. The nsp9 to nsp12 are involved in virus genome transcription and replication. The 3′ end of the viral genome encodes four minor and three major structural proteins. The GP2a, GP3 and GP4 (encoded by ORF2a, 3 and 4), are glycosylated membrane associated minor structural proteins. The fourth minor structural protein, the E protein (encoded by ORF2b), is an unglycosylated membrane associated protein. The viral envelope contains two major structural proteins: a glycosylated major envelope protein GP5 (encoded by ORF5) and an unglycosylated membrane M protein (encoded by ORF6). The third major structural protein is the nucleocapsid N protein (encoded by ORF7). All PRRSV non-structural and structural proteins are essential for virus replication, and PRRSV infectivity is relatively intolerant to subtle changes within the structural proteins. PRRSV virulence is multigenic and resides in both the non-structural and structural viral proteins. This review discusses the molecular characteristics, biological and immunological functions of the PRRSV structural and nsps and their involvement in the virus pathogenesis.
Elevated Risk of Carrying Gentamicin-Resistant Escherichia coli among U.S. Poultry Workers

Background Antimicrobial use in food-animal production is an issue of growing concern. The application of antimicrobials for therapy, prophylaxis, and growth promotion in broiler chicken production has been associated with the emergence and dissemination of antimicrobial-resistant enteric bacteria. Although human exposure to antimicrobial-resistant bacteria through food has been examined extensively, little attention has been paid to occupational and environmental pathways of exposure. Objective Our objective was to measure the relative risk for colonization with antimicrobial-resistant Escherichia coli among poultry workers compared with community referents. Methods We collected stool samples and health surveys from 16 poultry workers and 33 community referents in the Delmarva region of Maryland and Virginia. E. coli was cultured from stool samples, and susceptibility to ampicillin, ciprofloxacin, ceftriaxone, gentamicin, nitrofurantoin, and tetracycline was determined for each E. coli isolate. We estimated the relative risk for carrying antimicrobial-resistant E. coli among poultry workers compared with community referents. Results Poultry workers had 32 times the odds of carrying gentamicin-resistant E. coli compared with community referents. The poultry workers were also at significantly increased risk of carrying multidrug-resistant E. coli. Conclusions Occupational exposure to antimicrobial-resistant E. coli from live-animal contact in the broiler chicken industry may be an important route of entry for antimicrobial-resistant E. coli into the community.
On-line monitoring and diagnostics for power transformers

Transformers are a critical part of an electrical utility's asset base. Loss of a transformer in a utility, generation plant or process can cost many millions of dollars, depending on how long it is out-of-service. On-line monitoring and diagnostics is a useful tool to help operators to manage their assets and make decisions on continuing operation, maintenance or replacement.
Thoughts on the Ineffability of the Mystical Experience

Ineffability has been proposed as an important feature of the mystical experience. Various psychological processes may contribute to this ineffability, including expansion of awareness from center to margin of the field of consciousness (building on thoughts of William James and Frederic Myers); an attentional shift from a discrete figure to a large, complex, novel ground; limitations imposed by the nature of the "object" of the experience and by our vehicles of perception and cognition; difficulties of memory transfer from mystical to ordinary states of consciousness; and constraints imposed by brain structures, culture and tradition, and self-fulfilling prophesies. This focus on the limitations of vehicles of expression does not deny that exposure to a transcendent realm may also account for aspects of ineffability.
Identification and Validation of Evolutionarily Conserved Unusually Short Pre-mRNA Introns in the Human Genome

According to the length distribution of human introns, there is a large population of short introns with a threshold of 65 nucleotides (nt) and a peak at 85 nt. Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the identities of which are scarcely known. Here, we provide for the first time a list of bona fide human ultra-short introns, which have never been characterized elsewhere. By conducting BLAST searches of the databases, we screened 22 introns (37–65 nt) with conserved lengths and sequences among closely related species. We then provide experimental and bioinformatic evidence for the splicing of 15 introns, of which 12 introns were remarkably G-rich and 9 introns contained completely inefficient splice sites and/or branch sites. These unorthodox characteristics of ultra-short introns suggest that there are unknown splicing mechanisms that differ from the well-established mechanism.
Gene expression profiles in Ciona intestinalis stigmatal cells: Insight into formation of the ascidian branchial fissures

Gill slits, a series of openings in the pharyngeal epithelium, are characteristic features of the hemichordate and chordate body plans. In ascidians, these openings, called stigmata, are formed in the branchial sac during juvenile development. Multiple whole‐mount in situ hybridization analyses based on approximately 1,500 genes expressed in Ciona intestinalis juveniles, identified 28 genes expressed predominantly in the stigmatal cells. Expression patterns of these stigmatal genes were classified into four different categories. On the basis of these findings, we have been able to show that the peripheral region of a stigma consists of at least three different regions. The expression of a Dlk1‐like gene was detected in nonciliated cells during the stigma perforation and division and was maintained in the basal region of the elliptical stigma. Expression of meichroacidin, tektin A1, and tektin B1 orthologs during the differentiation of the ciliated stigmatal cells suggests that some of the molecular mechanisms involved in sperm differentiation might be recruited for the stigma development, or vice versa. Components of the cilia such as alpha‐tubulin and rootletin were also expressed in the stigmatal cells. These genes might facilitate further analyses regarding the evolution of the branchial fissures and the development of the ascidian stigmata. Developmental Dynamics 235:562–569, 2006. © 2005 Wiley‐Liss, Inc.
Occupational science: A new source of power for participants in occupational therapy

Abstract Occupational science is an emerging discipline which has the potential to support the practice and study of occupational therapy and contribute new knowledge to society. It originated in the values and traditions of occupational therapy as articulated by Adolph Meyer, the “occupational behavior” framework of Mary Reilly, the spirit of Jean Ayres’ clinical practice for children, and the work of a community of scholars at the University of Southern California. Occupational science is a new, interdisciplinary synthesis of basic knowledge concerning the human as an occupational being. Disciplines contributing to the science are identified according to their congruence with the root beliefs of occupational therapy. The core courses constituting the new doctor of philosophy degree in occupational science are described. Finally, assumptions supporting occupational science such as the importance of skill, holism, and an optimistic view of human nature are made explicit. Occupational science is a promisin.
Improving the Adaptability of AQM Algorithms to Traffic Load Using Fuzzy Logic

Adaptive RED (ARED) is an active queue management (AQM) designed for congestion responsive traffics such as TCP. ARED aims to keep average queue length around a predefined queue length. If so, average delay will be offered to Internet users and simultaneously high link utilization will be achieved. However, ARED algorithm merely makes the average queue length loosely converge to the target length with low responsiveness and low stability. One reason for this is that ARED uses a fixed increase step-size to adjust the maximum dropping probability to the current traffic load. In this paper, fuzzy logic (FL) controller has been designed to adaptively obtain the increase step-size of the maximum dropping probability based on the current traffic conditions. The simulation results show the proposed FL scheme improves the ARED’s adaptability to the current traffic loads, consequently achieving the desired target queue length with better performance than ARED, while keeping very similar drop rate and link utilization.
Recognising value tensions that underlie problems in inclusive education

This paper aims to examine some tensions that underlie inclusive education as regards pupils with disabilities and difficulties. Two key tensions are analysed: difference as enabling–stigmatising (dilemmas of difference) and participation–protection, both of which can lead to significant dilemmas. Berlin’s hedgehog–fox distinction about the unity (hedgehog view) or plurality (fox view) of values is adopted and extended to different positions about inclusion. More radical versions of inclusion are portrayed as expressing rigid hedgehog positions that commit to one big value and so ignore other important values. However, in veering to a fox perspective, the argument recognises the need for tensions to be resolved. This resolving tendency expresses an integrating aim that seeks a unified perspective, even if it is not a final and absolute one. In this way some balance between a unitary view (hedgehog view) and a plurality view (fox view) can be achieved.
Designing a unified programming model for heterogeneous machines

While high-efficiency machines are increasingly embracing heterogeneous architectures and massive multithreading, contemporary mainstream programming languages reflect a mental model in which processing elements are homogeneous, concurrency is limited, and memory is a flat undifferentiated pool of storage. Moreover, the current state of the art in programming heterogeneous machines tends towards using separate programming models, such as OpenMP and CUDA, for different portions of the machine. Both of these factors make programming emerging heterogeneous machines unnecessarily difficult. We describe the design of the Phalanx programming model, which seeks to provide a unified programming model for heterogeneous machines. It provides constructs for bulk parallelism, synchronization, and data placement which operate across the entire machine. Our prototype implementation is able to launch and coordinate work on both CPU and GPU processors within a single node, and by leveraging the GASNet runtime, is able to run across all the nodes of a distributed-memory machine.
Neural Network Based Pitch Tracking in Very Noisy Speech

Pitch determination is a fundamental problem in speech processing, which has been studied for decades. However, it is challenging to determinate pitch in strong noise because the harmonic structure is corrupted. In this paper, we estimate pitch using supervised learning, where the probabilistic pitch states are directly learned from noisy speech data. We investigate two alternative neural networks modeling pitch state distribution given observations. The first one is a feedforward deep neural network (DNN), which is trained on static frame-level acoustic features. The second one is a recurrent deep neural network (RNN) which is trained on sequential frame-level features and capable of learning temporal dynamics. Both DNNs and RNNs produce accurate probabilistic outputs of pitch states, which are then connected into pitch contours by Viterbi decoding. Our systematic evaluation shows that the proposed pitch tracking algorithms are robust to different noise conditions and can even be applied to reverberant speech. The proposed approach also significantly outperforms other state-of-the-art pitch tracking algorithms.
Popular Video Games: Quantifying the Presentation of Violence and Its Context

The aim of this study was to content analyze 60 of the most popular video games for violence from three gaming systems: Nintendo 64, Sega Dream- Cast, and Sony Playstation. Games were played for l0 minutes and videotaped for later content analysis. Adapting the coding scheme from the National Television Violence Study (Wilson et al., 7 997, 1998; Smith et al., 1998, the amount as well as the context of violence in games rated for general (e.g., "E" or "K-A") or mature audiences (e.g., "T" or "M") were assessed. The results show that mature games are more likely to feature violence than are those rated for general audiences. Differences also emerged in the context of violence. When compared to general audience games, mature games are not only more likely to feature child perpetrators but also justified acts of repeated gun violence that are graphic in nature. The findings are discussed in terms of the risks interactive violence may be posing to youth.
Expression of CNTF receptor-alpha in chick violet-sensitive cones with unique morphologic properties.

PURPOSE Application of ciliary neurotrophic factor (CNTF) can rescue mature photoreceptors from lesion-induced and hereditary degeneration. In the chick retina, expression of the CNTF receptor is present in a subpopulation of photoreceptor cells. The present study was undertaken to identify the CNTF receptor-expressing photoreceptors and to describe the subcellular localization of the receptor protein. METHODS The localization of the CNTF receptor was analyzed by light and electron microscopic immunocytochemistry in chick retinal wholemount preparations, with an antibody for CNTF receptor alpha (CNTFRalpha). Immunoreactive cells were identified by double labeling with immunocytochemical markers for photoreceptor subpopulations. RESULTS The CNTFRalpha antibody labeled evenly distributed outer segments (OS) of a photoreceptor subpopulation. CNTFRalpha-positive OS were associated with oil droplets of uniform size. Receptor immunoreactivity did not colocalize with markers for rods and red-green cones. Complete overlap was found after double labeling with the antibody CERN 933, which recognizes violet-sensitive cones in the chick retina. Ultrastructurally, the CNTFRalpha-immunoreactive OS showed rodlike properties: an elongated shape and stacks of membrane discs separated from the plasma membrane. Immunoreactivity was completely restricted to the plasma membrane of the OS and the inner membrane sheet of the photoreceptor calices present in avian retinas. CONCLUSIONS CNTFRalpha expression identifies a unique type of photoreceptors in the avian retina which does not fit into the classic morphologic definition of rods and cones. The specific expression in violet-sensitive photoreceptors suggests that CNTF may have a neuroprotective role related to the specific function of these cells.
Para‐cresyl sulfate acutely impairs vascular reactivity and induces vascular remodeling

Chronic kidney disease (CKD) is characterized by vascular remodeling and the retention of uremic toxins, several of which are independently associated with the high cardiovascular mortality rate in CKD patients. Whether the association between these uremic toxins and cardiovascular mortality is due to induction of vascular dysfunction and resulting vascular remodeling remains to be determined. This study evaluates the effects of para‐cresyl sulfate (PCS), a newly identified uremic toxin, on vascular function and remodeling. PCS acutely induced oxidative stress in both endothelial and vascular smooth muscle cells, with a maximal effect at 0.15 mM, corresponding to the mean “uremic” concentration found in dialysis patients. PCS significantly increased within 30 min phenylephrine‐induced contraction of mouse thoracic aorta, through direct activation of rho‐kinase, independently of oxidative stress induction, as demonstrated by the capacity of rho‐kinase inhibitor Y‐27632 to abolish this effect. After exposure of the aorta to PCS for 48 h, we observed inward eutrophic remodeling, a hallmark of uremic vasculopathy characterized by a reduction of the area of both lumen and media, with unchanged media/lumen ratio. In conclusion, elevated PCS concentrations such as those observed in CKD patients, by promoting both vascular dysfunction and vascular remodeling, may contribute to the development of hypertension and to cardiovascular mortality in CKD. J. Cell. Physiol. 230: 2927–2935, 2015. © 2015 Wiley Periodicals, Inc.
Synthetic speaker models using VTLN to improve the performance of children in mismatched speaker conditions for ASR

The paper proposes to train synthetic speaker models using vocal tract length normalization (VTLN). Speaker adaptation based approaches require certain amount of data from the test speaker to either update or transform the model parameters of the trained model. If there is very little or no data available from the test speaker, we propose to create a synthetic speaker model that is acoustically close to the test speaker by scaling the training data with VTLN. For this purpose, we train multiple VTLN warped speaker independent (SI) models by scaling the training data with VTLN and choosing one of the models that is acoustically close to the test speaker for performing recognition. We show that the proposed approach is advantageous in mismatched speaker conditions, especially while recognizing children speakers using models trained on adult speech.
The Clinical Significance of Exercise‐induced ST‐segment Elevation

SUMMARY The significance of exercise-induced ST-segment elevation remains unsettled. We reviewed the treadmill tests of 840 consecutive patients and exercise-induced ST-segment elevation was noted in 29 (3.5%). Only eight of these (28%) stopped because of angina. Anterior myocardial infarction (AMI) was found on the resting electrocardiogram in 25 (85%). Angiographic studies performed on 21 showed critical lesions. of the left anterior descending (LAD) in 19 (90%) and left ventricular aneurysm in 18 (86%). When all the patients who had AMI or critical LAD obstruction during the study period were reviewed, only 22&percnt and 18&percnt respectively showed exercise-induced ST-segment elevation, while 64&percnt of the cases with left ventricular aneurysm displayed this phenomenon. Thus, exercise-induced ST elevation seems to reflect the presence of severe coronary artery disease most commonly with an associated left ventricular aneurysm and may relate more to the abnormal wall motion than to the myocardial ischemia.per se.
Progress in understanding grief, complicated grief, and caring for the bereaved

Abstract Grief occurs with loss of symbolically important connections and involves intense emotional reactions and changes to our experiences of self, the world, and the future.Individual responses reflect factors such as personality and life history, social context and cultural practices, and the symbolic magnitude of the loss. Grieving can be a relatively slow and uneven process, so applying prescriptive stages or goals to individuals‘ experiences can be unhelpful. Although most people are resilient in the face of loss and do not require special interventions, health professionals can contribute by empathic use of communication skills to facilitate the grieving process. A minority will struggle with their grief and experience prolonged, intense, or problematic reactions. Psychiatric comorbidities including depression and anxiety disorders can occur, and a distinct diagnosis of complicated grief disorder has been proposed. Health professionals can identify complicated grief reactions and ensure patients receive specialised treatment, including intensive grief therapy and medication where indicated. Assessment methods are summarised to assist health professionals in providing a continuum of care for those who are grieving.
Does long in vitro culture promote large for gestational age babies?

STUDY QUESTION Does the length of time during which embryos are cultured in vitro affect the birthweight of the infants? SUMMARY ANSWER The duration of the embryo culture period is a significant factor in determining the birthweight of the infants. WHAT IS ALREADY KNOWN IVF children show adverse perinatal outcome when compared with the general population and increased incidence of preterm birth and low birthweight is commonly observed. STUDY DESIGN, SIZE, DURATION A retrospective cross-sectional cohort study including 1079 infants born after treatment at the Family Federation of Finland Fertility Clinic in Helsinki, between 2000 and 2010. PARTICIPANTS, SETTING, METHODS All singleton IVF children were included. The gestation- and gender-adjusted birthweights of the babies were analyzed according to mother's age, BMI, and parity, type of treatment (IVF or ICSI), main cause of infertility and embryo culture period. Two outcomes were investigated: the birthweight and the proportion of small and large for gestational age (SGA and LGA) infants. Multiple linear regression analysis was performed to show the significance of each individual factor on determining the birthweight of the babies born. MAIN RESULTS AND THE ROLE OF CHANCE In the study group as a whole, the distribution of the SGA and LGA babies showed no deviation from the growth charts of the general population. However, when the birthweight of the children was analyzed according to the length of embryo culture from Day 2 to Days 5-6, an increase in the proportion of LGA babies was found (D2 9.4%, D3 11.5%, D5-6 18.8%; D2 n = 871, D3 n = 139, D5-6 n = 69). Multiple linear regression analysis showed that BMI (P < 0.001) and parity (P < 0.001) of the mother, as well as the embryo culture period (P = 0.007) had a significant effect on the birthweight. The value of the adjusted R(2) was 0.437. LIMITATIONS, REASONS FOR CAUTION Small number of D5-6 infants and a lack of pregnancy-associated factors contributing to birthweight. WIDER IMPLICATIONS OF THE FINDING This study warrants larger studies to analyze the birthweight of the IVF children, particularly after blastocyst culture. STUDY FUNDING/COMPETING INTEREST The study was funded by the Family Federation of Finland, Fertility Clinic Helsinki. No competing interests.