Miracle-dz/UniFAR-FTUs huggingface dataset:
Fibre type-specific expression patterns of myosin heavy chain genes in adult torafugu Takifugu rubripes muscles

SUMMARY Comprehensive in silico studies, based on the total fugu genome database, which was the first to appear in fish, revealed that torafugu Takifugu rubripes contains 20 sarcomeric myosin heavy chain (MYH) genes (MYH genes) (Ikeda et al., 2007). The present study was undertaken to identify MYH genes that would be expressed in adult muscles. In total, seven MYH genes were found by screening cDNA clone libraries constructed from fast, slow and cardiac muscles. Three MYH genes, fast-type MYHM86-1, slow-type MYHM8248 and slow/cardiac-type MYHM880, were cloned exclusively from fast, slow and cardiac muscles, respectively. Northern blot hybridization substantiated their specific expression, with the exception of MYHM880. In contrast, transcripts of fast-type MYHM2528-1 and MYHM1034 were found in both fast and slow muscles as revealed by cDNA clone library and northern blot techniques. This result was supported by in situ hybridization analysis using specific RNA probes, where transcripts of fast-type MYHM2528-1 were expressed in fast fibres with small diameters as well as in fibres of superficial slow muscle with large diameters adjacent to fast muscle. Transcripts of fast-type MYHM86-1 were expressed in all fast fibres with different diameters, whereas transcripts of slow-type MYHM8248 were restricted to fibres with small diameters located in a superficial part of slow muscle. Interestingly, histochemical analyses showed that fast fibres with small diameters and slow fibres with large diameters both contained acid-stable myofibrillar ATPase, suggesting that these fibres have similar functions, possibly in the generation of muscle fibres irrespective of their fibre types.
Benkler Revisited - Venturing beyond the Open Source Software Arena?

The organizational principles of open source software (OSS) development have challenged traditional theories in economics, organization research and information systems. In a seminal paper, Benkler (2002) provided a comprehensive framework to structure and explain these OSS principles. Coined Commons-Based Peer Production (CBPP), his framework has inspired a large stream of research on OSS. The objective of our paper is to determine whether CBPP also provides a viable framework to investigate projects of open innovation in non-software related domains. Using a case study approach, we focus on four projects that attempt to operate in line with the OSS phenomenon, but deal with tangible outputs (biotechnology, automobiles, entertainment hardware, and public patent review). We show that in general the CBPP framework is well-suited to explain "open" value creation in these domains. However, we also find several factors which limit its adoption to non-software related arenas.
Costal cartilage tracheoplasty for congenital long-segment tracheal stenosis.

OBJECTIVES To evaluate and report the outcome of costal cartilage tracheoplasty for the treatment of congenital long-segment tracheal stenosis. DESIGN Retrospective chart review. SETTING Academic tertiary care children's hospital. PATIENTS Consecutive series of 10 patients who presented with congenital long-segment tracheal stenosis. INTERVENTION All patients underwent costal cartilage tracheoplasty while receiving cardiopulmonary bypass. MEASUREMENTS Age at repair, weight at repair, length of stenosis, minimal diameter of stenosis, postoperative days receiving ventilator support, postoperative days until discharge, postoperative bronchoscopies, postoperative complications, associated anomalies, survival rate, and current status. RESULTS There were 8 males and 2 females with an average age at repair of 18 weeks. Average weight was 5.2 kg. Average length of stenosis was 3.2 cm, and average minimal diameter was 1.9 mm. Average postoperative days receiving ventilator support was 17 with a median of 9.5. Average postoperative days until discharge was 35.2 with a median of 17. Average postoperative bronchoscopies was 18 with a median of 4.5. There was a 40% major postoperative complication rate. Seven of the patients had associated anomalies. No patient died from an inadequate tracheal airway, though 2 patients ultimately died from other cardiopulmonary complications for a survival rate of 80%. Average time since surgery for survivors is 8.0 years. Two patients still require treatment. Seven of the original 10 patients are fully active without tracheostomy. CONCLUSION We report one of the largest series of costal cartilage tracheoplasty for congenital long-segment tracheal stenosis and one that has met with a relatively high success rate.
MicroRNAs 9 and 370 Association with Biochemical Markers in T2D and CAD Complication of T2D

Background MicroRNAs (miRNAs) are small non coding RNAs with essential roles, of which any alteration leads to several conditions. Their roles in diabetes (DM) and its vascular complications have not been completely assessed. Aim to study the association of two miRNAs; 9 and 370, with biochemical parameters of type 2 diabetic (T2D), dyslipidemia and coronary artery disease (CAD). Subjects and Methods Blood samples were taken from 200 subjects of both genders, in the Outpatient clinic of Al Qasr El-Einy teaching hospitals, in which levels of both miRNAs (using real time PCR) and routine parameters were measured. Subjects were divided over four groups, 50 in each group as follows; patients with T2D, patients with CAD, patients with T2D and CAD, and healthy control subjects. Main Outcome miRNA 9 levels were expected to be over expressed in diabetic patients, while miRNA 370 levels were expected to be over expressed in those suffering from CAD and their association with CAD complication of T2D. Results miRNA 9 levels were significantly higher in T2D patients and T2D patients with CAD, (1.18±0.07, and 1.31±0.08 respectively), while miRNA 370 levels were significantly higher in T2D patients, CAD patients, and T2D patients with CAD (0.59±0.05, 1.00±0.05, and 1.20±0.06 respectively), compared to control group at p = 0.000. In addition both miRNAs were still significantly associated with each other even after conducting multiple regression analysis. Conclusion This study associates the possible role of miRNAs in the diagnosis/prognosis of CAD complication of T2D.
An Analysis of the Effects of Acetylcholine on Conduction and Refractoriness in the Rabbit Sinus Node

The effects of acetylcholine (ACh) on sinus node automaticity, atrio-sinus conduction, and refractoriness were studied in 41 isolated rabbit right atrial preparations. Average control rate was 126 beats/min, and ACh 5 × 10−8 M, 5 × 10−7 M, and 5 × 10−7 M significantly decreased heart rate by 7, 15, and 43%, respectively (P < 0.01, 0.001, and 0.001). Atrio-sinus conduction time at a pacing cycle length of 400 msec did not significantly change during exposure to ACh 5 x 10−8 and 5 × 10−7 M. However, the mean effective refractory period (ERP) of the sinus node, at a pacing cycle length of 400 msec, increased from 183 ± 16 msec to 210 ± 24 msec during exposure to ACh 5 x 10−7 M (P< 0.025). The change in ERP followed the change in action potential duration. In contrast to the lack of effect of ACh 5 x 10−7 M on atrio-sinus conduction time, ACh 5 x 10−6 M caused 2:1 atrio-sinus block in 8 of 10 experiments. The site of block was identified using multiple microelectrode impalements, and occurred between the perinodal fibers bordering on the edge of the sinus node and the pacemaker area in the sinus node proper. When the pacing cycle length was increased and 1:1 atrio-sinus conduction was present, conduction time did not significantly differ from control. At this longer pacing cycle length the mean ERP of the sinus node was 380 msec greater than control and lasted well after repolarization was completed. Thus, atrio-sinus block during exposure to ACh 5 x 10−6 M resulted from a marked prolongation of refractoriness. Circ Res 44: 112-120, 1979
On-Line Sequential Extreme Learning Machine

The primitive Extreme Learning Machine (ELM) [1, 2, 3] with additive neurons and RBF kernels was implemented in batch mode. In this paper, its sequential modification based on recursive least-squares (RLS) algorithm, which referred as Online Sequential Extreme Learning Machine (OS-ELM), is introduced. Based on OS-ELM, Online Sequential Fuzzy Extreme Learning Machine (Fuzzy-ELM) is also introduced to implement zero order TSK model and first order TSK model. The performance of OS-ELM and Fuzzy-ELM are evaluated and compared with other popular sequential learning algorithms, and experimental results on some real benchmark regression problems show that the proposedOnlineSequentialExtreme Learning Machine (OS-ELM) produces better generalization performance at very fast learning speed.
CAUSES: Diagnosis of the Summertime Warm Bias in CMIP5 Climate Models at the ARM Southern Great Plains Site

All the weather and climate models participating in the Clouds Above the United States and Errors at the Surface project show a summertime surface air temperature (T2 m) warm bias in the region of the central United States. To understand the warm bias in long‐term climate simulations, we assess the Atmospheric Model Intercomparison Project simulations from the Coupled Model Intercomparison Project Phase 5, with long‐term observations mainly from the Atmospheric Radiation Measurement program Southern Great Plains site. Quantities related to the surface energy and water budget, and large‐scale circulation are analyzed to identify possible factors and plausible links involved in the warm bias. The systematic warm season bias is characterized by an overestimation of T2 m and underestimation of surface humidity, precipitation, and precipitable water. Accompanying the warm bias is an overestimation of absorbed solar radiation at the surface, which is due to a combination of insufficient cloud reflection and clear‐sky shortwave absorption by water vapor and an underestimation in surface albedo. The bias in cloud is shown to contribute most to the radiation bias. The surface layer soil moisture impacts T2 m through its control on evaporative fraction. The error in evaporative fraction is another important contributor to T2 m. Similar sources of error are found in hindcast from other Clouds Above the United States and Errors at the Surface studies. In Atmospheric Model Intercomparison Project simulations, biases in meridional wind velocity associated with the low‐level jet and the 500 hPa vertical velocity may also relate to T2 m bias through their control on the surface energy and water budget.
Terahertz Line Defect Waveguide Based on Silicon-on-Glass Technology

In this paper, based on silicon-on-glass technology, a new THz dielectric waveguide structure is proposed. The proposed waveguide is low loss, and has a mechanically stable structure. The new waveguide is scalable to higher frequencies in THz band. Theoretical and experimental results for 500 to 700 GHz frequency range are presented. The introduced waveguide can be a platform for highly sensitive integrated THz sensors.
DUPLO: Unifying Cut-and-Choose for Garbled Circuits

Cut-and-choose (CC) is the standard approach to making Yao's garbled circuit two-party computation (2PC) protocol secure against malicious adversaries. Traditional cut-and-choose operates at the level of entire circuits, whereas the LEGO paradigm (Nielsen & Orlandi, TCC 2009) achieves asymptotic improvements by performing cut-and-choose at the level of individual gates. In this work we propose a unified approach called DUPLO that spans the entire continuum between these two extremes. The cut-and-choose step in our protocol operates on the level of arbitrary circuit "components," which can range in size from a single gate to the entire circuit itself. With this entire continuum of parameter values at our disposal, we find that the best way to scale 2PC to computations of realistic size is to use CC components of intermediate size, and not at the extremes. On computations requiring several millions of gates or more, our more general approach to CC gives between 4-7x improvement over existing approaches. In addition to our technical contributions of modifying and optimizing previous protocol techniques to work with general CC components, we also provide an extension of the recent Frigate circuit compiler (Mood et al, Euro S&P 2016) to effectively express any C-style program in terms of components which can be processed efficiently using our protocol.
CRY2 Is Associated with Rapid Cycling in Bipolar Disorder Patients

Background Bipolar disorder patients often display abnormalities in circadian rhythm, and they are sensitive to irregular diurnal rhythms. CRY2 participates in the core clock that generates circadian rhythms. CRY2 mRNA expression in blood mononuclear cells was recently shown to display a marked diurnal variation and to respond to total sleep deprivation in healthy human volunteers. It was also shown that bipolar patients in a depressive state had lower CRY2 mRNA levels, nonresponsive to total sleep deprivation, compared to healthy controls, and that CRY2 gene variation was associated with winter depression in both Swedish and Finnish cohorts. Principal Findings Four CRY2 SNPs spanning from intron 2 to downstream 3′UTR were analyzed for association to bipolar disorder type 1 (n = 497), bipolar disorder type 2 (n = 60) and bipolar disorder with the feature rapid cycling (n = 155) versus blood donors (n = 1044) in Sweden. Also, the rapid cycling cases were compared with bipolar disorder cases without rapid cycling (n = 422). The haplotype GGAC was underrepresented among rapid cycling cases versus controls and versus bipolar disorder cases without rapid cycling (OR = 0.7, P = 0.006−0.02), whereas overrepresentation among rapid cycling cases was seen for AAAC (OR = 1.3−1.4, P = 0.03−0.04) and AGGA (OR = 1.5, P = 0.05). The risk and protective CRY2 haplotypes and their effect sizes were similar to those recently suggested to be associated with winter depression in Swedes. Conclusions We propose that the circadian gene CRY2 is associated with rapid cycling in bipolar disorder. This is the first time a clock gene is implicated in rapid cycling, and one of few findings showing a molecular discrimination between rapid cycling and other forms of bipolar disorder.
Predatory Efficacy of Culex (Lutzia) Fuscanus on Mosquito Vectors of Human Diseases in Sri Lanka

Abstract Larvae of Culex (Lutzia) fuscanus were collected from ovitraps in a natural breeding site. Collected larvae were used to establish a self-mating colony, and larval progeny were then used to determine their predatory efficacy on larvae of 3 vector mosquito species, Aedes aegypti, Anopheles subpictus, and Cx. tritaeniorhynchus. Statistical analysis revealed that Cx. fuscanus showed greater feeding efficacy for Ae. aegypti than for Cx. tritaeniorhynchus and An. subpictus. The natural predatory role of this species can potentially be exploited for biological control of mosquito vectors in Sri Lanka.
Omics Pipe: a community-based framework for reproducible multi-omics data analysis

MOTIVATION Omics Pipe (http://sulab.scripps.edu/omicspipe) is a computational framework that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole-Genome sequencing, ChIP-seq analyses and automatic processing of data from The Cancer Genome Atlas (TCGA). Omics Pipe provides researchers with a tool for reproducible, open source and extensible next generation sequencing analysis. The goal of Omics Pipe is to democratize next-generation sequencing analysis by dramatically increasing the accessibility and reproducibility of best practice computational pipelines, which will enable researchers to generate biologically meaningful and interpretable results. RESULTS Using Omics Pipe, we analyzed 100 TCGA breast invasive carcinoma paired tumor-normal datasets based on the latest UCSC hg19 RefSeq annotation. Omics Pipe automatically downloaded and processed the desired TCGA samples on a high throughput compute cluster to produce a results report for each sample. We aggregated the individual sample results and compared them to the analysis in the original publications. This comparison revealed high overlap between the analyses, as well as novel findings due to the use of updated annotations and methods. AVAILABILITY AND IMPLEMENTATION Source code for Omics Pipe is freely available on the web (https://bitbucket.org/sulab/omics_pipe). Omics Pipe is distributed as a standalone Python package for installation (https://pypi.python.org/pypi/omics_pipe) and as an Amazon Machine Image in Amazon Web Services Elastic Compute Cloud that contains all necessary third-party software dependencies and databases (https://pythonhosted.org/omics_pipe/AWS_installation.html).
Do common frogs (Rana temporaria) follow Bergmann's rule?

Questions: Does intraspecific extension of Bergmanns rule – larger size within a species in cooler areas – hold true for ectotherms in general, and for the common frog (Rana temporaria) in particular? What is the relative importance of genetic and environmental factors (i.e. direct environmental induction) in determining latitudinal patterns of body size variation in common frogs? Methods: We tested for a positive association between mean body size and latitude in common frogs (Rana temporaria) across a 1600 km long latitudinal gradient in Scandinavia both for wild-collected adults and laboratory-reared metamorphs. Results: In adults, the mean body size increased from south to mid-latitudes, and declined thereafter. This occurred despite the fact that the mean age of adult frogs increased with increasing latitude, and age and body size were positively correlated. The latitudinal pattern of body size variation in metamorphs reared in a common garden experiment was similar to that observed among wild-caught adults. Conclusions: The results suggest that the concave pattern of body size variation across the latitudinal cline may be at least partly genetically determined, and that although there is considerable geographic variation in mean body size of R. temporaria, this variation does not conform with Bergmann’s rule.
Right-to-left shunt has modest effects on CO2 delivery to the gut during digestion, but compromises oxygen delivery

ABSTRACT By virtue of their cardiovascular anatomy, reptiles and amphibians can shunt blood away from the pulmonary or systemic circuits, but the functional role of this characteristic trait remains unclear. It has been suggested that right-to-left (R–L) shunt (recirculation of systemic blood within the body) fuels the gastric mucosa with acidified and CO2-rich blood to facilitate gastric acid secretion during digestion. However, in addition to elevating PCO2, R–L shunt also reduces arterial O2 levels and would compromise O2 delivery during the increased metabolic state of digestion. Conversely, arterial PCO2 can also be elevated by lowering ventilation relative to metabolism (i.e. reducing the air convection requirement, ACR). Based on a mathematical analysis of the relative roles of ACR and R–L shunt on O2 and CO2 levels, we predict that ventilatory modifications are much more effective for gastric CO2 supply with only modest effects on O2 delivery. Conversely, elevating CO2 levels by means of R–L shunt would come at a cost of significant reductions in O2 levels. The different effects of altering ACR and R–L shunt on O2 and CO2 levels are explained by the differences in the effective blood capacitance coefficients. Summary: Shunting in reptiles is ineffective for regulating gastric CO2 supply but effectively reduces blood O2 levels.
A Generalized Stochastic Variational Bayesian Hyperparameter Learning Framework for Sparse Spectrum Gaussian Process Regression

While much research effort has been dedicated to scaling up sparse Gaussian process (GP) models based on inducing variables for big data, little attention is afforded to the other less explored class of low-rank GP approximations that exploit the sparse spectral representation of a GP kernel. This paper presents such an effort to advance the state of the art of sparse spectrum GP models to achieve competitive predictive performance for massive datasets. Our generalized framework of stochastic variational Bayesian sparse spectrum GP (sVBSSGP) models addresses their shortcomings by adopting a Bayesian treatment of the spectral frequencies to avoid overfitting, modeling these frequencies jointly in its variational distribution to enable their interaction a posteriori, and exploiting local data for boosting the predictive performance. However, such structural improvements result in a variational lower bound that is intractable to be optimized. To resolve this, we exploit a variational parameterization trick to make it amenable to stochastic optimization. Interestingly, the resulting stochastic gradient has a linearly decomposable structure that can be exploited to refine our stochastic optimization method to incur constant time per iteration while preserving its property of being an unbiased estimator of the exact gradient of the variational lower bound. Empirical evaluation on real-world datasets shows that sVBSSGP outperforms state-of-the-art stochastic implementations of sparse GP models.
Classification of psychotic symptoms in dementia with Lewy bodies.

OBJECTIVE The aim of this study is to determine empirically a possible classification of psychotic symptoms, and identify the frequency of such symptoms in dementia with Lewy bodies (DLB). METHODS This was a clinical study of prospectively observed patients from the memory clinic at Shiga Medical Center. The authors conducted a factor analysis of psychotic symptoms in 96 probable DLB and 4 possible DLB patients, clinically diagnosed according to the consensus criteria, were included. RESULTS Four factors were obtained. Factor 1 was closely akin to misidentifications, including Capgras syndrome, phantom boarder, and reduplication of people and places. Factor 2 consisted of reduplication of people, the belief that deceased relatives are still alive, and the belief that absent relatives are in the house, which was classified as a type of misidentification or paramnesia. Factor 3 was akin to visual hallucinations of nonhuman objects, and factor 4 mirrored the hallucination of people and feeling of presence. Delusions were independent of these factors. Following the results of factor analysis, the rates of each symptom group were identified. Hallucinations were the most frequent psychotic symptom in DLB (78%), followed by misidentifications (56%) and delusions (25%). CONCLUSION This study suggested that hallucinations, misidentifications, and delusions should be separately considered in understanding of underlying pathophysiology or psychopathology of DLB.