Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding Fault Scenarios and Impacts through Fault Injection Experiments in Cielo

We present a set of fault injection experiments performed on the ACES (LANL/SNL) Cray XE supercomputer Cielo. We use this experimental campaign to improve the understanding of failure causes and propagation that we observed in the field failure data analysis of NCSA's Blue Waters. We use the data collected from the logs and from network performance counter data 1) to characterize the fault-error-failure sequence and recovery mechanisms in the Gemini network and in the Cray compute nodes, 2) to understand the impact of failures on the system and the user applications at different scale, and 3) to identify and recreate fault scenarios that induce unrecoverable failures, in order to create new tests for system and application design. The faults were injected through special input commands to bring down network links, directional connections, nodes, and blades. We present extensions that will be needed to apply our methodologies of injection and analysis to the Cray XC (Aries) systems.
Fused Text Segmentation Networks for Multi-oriented Scene Text Detection

In this paper, we introduce a novel end-end framework for multi-oriented scene text detection from an instance-aware semantic segmentation perspective. We present Fused Text Segmentation Networks, which combine multi-level features during the feature extracting as text instance may rely on finer feature expression compared to general objects. It detects and segments the text instance jointly and simultaneously, leveraging merits from both semantic segmentation task and region proposal based object detection task. Not involving any extra pipelines, our approach surpasses the current state of the art on multi-oriented scene text detection benchmarks: ICDAR2015 Incidental Scene Text and MSRA-TD500 reaching Hmean 84.1 % and 82.0 % respectively. Morever, we report a baseline on total-text containing curved text which suggests effectiveness of the proposed approach.
Subcellular distribution of low‐voltage activated T‐type Ca2+ channel subunits (Cav3.1 and Cav3.3) in reticular thalamic neurons of the cat

Low‐voltage‐activated (LVA) Ca2+ channels play a critical role in the generation of burst firing in the thalamus. Recently, three LVA Ca2+ channel isoforms (Cav3.1, Cav3.2, Cav3.3) have been identified in the reticular thalamic nucleus (RE). Previous electrophysiological and modelling studies have suggested that kinetically different T‐type channels might be expressed in a compartmentalized manner in RE cells. However, their precise subcellular distribution has not been fully elucidated. Using light and electron microscopic (EM) immunocytochemistry, we investigated the subcellular expression pattern of Cav3.1 and Cav3.3 channel subunits in RE neurons of the cat. Fluorescent and peroxidase labelling demonstrated the presence of Cav3.1 channel predominantly on the somata and proximal dendrites and Cav3.3 channels on cell bodies. Quantitative immunogold localization disclosed that Cav3.1 and Cav3.3 isoforms showed 5.8‐ and 8.7‐fold higher density, respectively, in the cytoplasm compared with somatic plasma membrane. Density of Cav3.1 isoform in the somatic plasma membrane was 2.21‐fold higher compared with Cav3.3 subunit. In the dendritic plasma membrane, Cav3.1 channel isoform was expressed throughout the entire dendritic tree. In contrast, Cav3.3 isoform was absent from large‐caliber, presumably proximal dendritic segments. Quantitative comparison showed that the relative density of immunogold particles compared with dendritic surface was 8.9‐ and 14.8‐fold higher for Cav3.1 and Cav3.3, respectively, in small‐diameter dendrites than in large proximal dendritic segments or somata. Our results demonstrate a higher density of low‐threshold Ca2+ channels in distal dendrites and provide further evidence of the role of RE neuron dendrites in the generation of prolonged, low‐threshold spike bursts. © 2009 Wiley‐Liss, Inc.
Alteration of phospholipid composition by combined defects in phosphatidylserine and cardiolipin synthases and physiological consequences in Escherichia coli

Escherichia coli K-12 derivatives with a common genetic background carrying, either alone or in combination, the pss-1 allele coding for a temperature-sensitive phosphatidylserine synthase (A. Ohta and I. Shibuya, J. Bacteriol. 132:434-443, 1977) and cls- for a defective cardiolipin synthase (G. Pluschke et al., J. Biol. Chem. 253:5048-5055, 1978) were constructed. The phospholipid polar headgroup compositions of these strains were significantly different from each other depending on their genotypes and growth temperature, whereas other membrane characteristics such as the total phospholipid content, fatty acid composition, membrane protein profile, and lipopolysaccharide content were practically the same, suggesting that the phenotypes of these strains were the direct consequences of abnormalities in membrane phospholipid composition. The cls pss-1 double mutation caused an unusual accumulation of phosphatidylglycerol with an extremely low content of cardiolipin. The cls mutation alone was found to give a growth defect, and its introduction into a pss-1 mutant resulted in an enhanced temperature sensitivity of growth. Addition to a broth medium of a proper concentration of sucrose, NaCl, Mg2+, or Ca2+ allowed the growth of a pss-1 mutant at otherwise nonpermissive temperature, but a pss-1 cls double mutant required the combined addition of sucrose or NaCl and MgCl2 for full growth at 42 degrees C. The possible mechanisms for these physiological consequences of the mutations are discussed on a molecular basis. The remedial effects of culture supplements allowed the pss-1 mutants to grow at 42 degrees C resulting in enhanced abnormalities of membrane phospholipid composition.
Perpendicular Magnetic Anisotropy in Heusler Alloy Films and Their Magnetoresistive Junctions

For the sustainable development of spintronic devices, a half-metallic ferromagnetic film needs to be developed as a spin source with exhibiting 100% spin polarisation at its Fermi level at room temperature. One of the most promising candidates for such a film is a Heusler-alloy film, which has already been proven to achieve the half-metallicity in the bulk region of the film. The Heusler alloys have predominantly cubic crystalline structures with small magnetocrystalline anisotropy. In order to use these alloys in perpendicularly magnetised devices, which are advantageous over in-plane devices due to their scalability, lattice distortion is required by introducing atomic substitution and interfacial lattice mismatch. In this review, recent development in perpendicularly-magnetised Heusler-alloy films is overviewed and their magnetoresistive junctions are discussed. Especially, focus is given to binary Heusler alloys by replacing the second element in the ternary Heusler alloys with the third one, e.g., MnGa and MnGe, and to interfacially-induced anisotropy by attaching oxides and metals with different lattice constants to the Heusler alloys. These alloys can improve the performance of spintronic devices with higher recording capacity.
A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK

Objective:Antiretroviral-naive HIV-positive individuals contribute to the transmission of drug-resistant viruses, compromising first-line therapy. Using phylogenetic inference, we quantified the proportion of transmitted drug-resistance originating from a treatment-naive source. Methods:Using a novel phylotype-based approach, 24 550 HIV-1 subtype B partial pol gene sequences from the UK HIV Drug Resistance database were analysed. Ongoing transmission of drug resistance amongst HIV-positive individuals was identified as phylotypes of at least three sequences with at least one shared drug resistance mutation, a maximum intra-clade genetic distance of 4.0% and a basal branch support at least 90%. The time of persistence of the transmission chains was estimated using a fast least-squares molecular clock inference approach. Results:Around 70% of transmitted drug-resistance had a treatment-naive source. The most commonly transmitted mutations were L90M in the protease gene and K103N, T215D and T215S in reverse transcriptase. Reversion to wild type occurred at a low frequency and drug-independent reservoirs of resistance have persisted for up to 13 years. Conclusion:These results illustrate the impact of viral fitness on the establishment of resistance reservoirs and support the notion that earlier diagnoses and treatment of HIV infections are warranted for counteracting the spread of antiretroviral resistance. Phylotype-based phylogenetic inference is an attractive approach for the routine surveillance of transmitted drug resistance in HIV as well as in other pathogens for which genotypic resistance data are available.
The analysis of odor character of cooked silver carp muscles using gas chromatography-mass spectrometry and gas chromatography-olfactometry

Volatile compounds of cooked sliver carp muscles extracted by simultaneous distillation and extraction (SDE) and solid phase microextraction (SPME) were analyzed by gas chromatography-mass spectrometry (GC-MS) and gas chromatography-olfactometry (GC-O). GC-MS results indicated that total 85 volatile flavor compounds were identified, including aldehydes, alcohols, ketones, acids, esters, hydrocarbons and heterocyclic compounds. SPME provided better extraction for a lower molecular mass, and SDE provided better extraction for a higher molecular mass. GC-O results indicated that total 23 odor character compounds were identified, aldehydes were the important odor compounds. More detailed compositions of volatile compounds and odor character of cooked sliver carp muscles could be identified by GC-MS combined with GC-O.
Beyond parent management: The role of students and schools in Philadelphia's high school "choice" process

This dissertation is a multiple methods study that examines the role of both students and schools in Philadelphia’s high school application process. First, district administrative data of a cohort of eighth grade students in 2008-09 and school characteristics is used to examine students’ odds of high school application and admission. A two-level hierarchical generalized linear model is used to account for the clustering of students within sending schools and to determine the relative contribution of individual and school characteristics. Students who meet the seventh grade record criteria have higher odds of application and admission, but race, gender, special education status, and English language learner (ELL) status are also significant predictors. Further, students in K-8 schools have higher odds of application, and students in high poverty and persistently dangerous schools have lower odds of admission, controlling for other factors. Second, interview data of sending school counselors, parents, and students and observations of high schoolrelated activities at 10 schools is used to answer questions about who manages the application process. Counselors employed two distinct strategies. In the “clearinghouse approach,” counselors were willing to help students, but the burden of information and decision-making is on families. In contrast, counselors who used the “brokering approach” raise students’ high school awareness in seventh grade and meet individually with students and their parents in eighth grade to decide where the child should apply, given their seventh grade record and interests. Students whose parents have less than high school education and students from immigrant families particularly benefit from the institutional supports of the brokering approach because they otherwise navigate the high school application process independently. Thus, the counselor approach is one mechanism through which schools can mitigate or exacerbate individual differences in information and the likelihood of high school application and admission. Overall, this study reveals that individual and sending school characteristics matter more than the school choice literature suggests. Students’ seventh grade record limits their high school options, but students with equal qualifications have unequal odds of admission in this system based on their background characteristics and school characteristics. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Education First Advisor Grace Kao This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/214 Second Advisor Rebecca Maynard Third Advisor Annette Lareau
Therapeutic effect of osthole on hyperlipidemic fatty liver in rats

AbstractAim:To study the effects of osthole on hyperlipidemic fatty liver and investigate the possible mechanisms.Methods:A rat model with hyperlipidemic fatty liver was successfully established by feeding fatty milk for 6 weeks. The experimental rats were then treated with 5-20 mg/kg osthole for 6 weeks. The mouse hyperlipidemic model was induced by feeding fatty milk when they were treated with 10-20 mg/kg osthole for 3 weeks.Results:After treatment with osthole, the levels of rat serum total cholesterol (TC), triglyceride (TG) and low density lipoprotein-cholesterol significantly decreased as compared with the fatty liver model group (P<0.05 or P<0.01). Hepatic weight and its coefficient, the hepatic tissue contents of TC, TG, and malondialdehyde, also significantly decreased (P<0.05 or P<0.01). In fatty milk-induced hyperlipidemic mice, the post-heparin plasma activities of lipo-protein lipase (LPL), hepatic lipase (HL), and total lipase (TL) significantly increased after treatment with 10-20 mg/kg osthole for 3 weeks (P<0.05 or P<0.01). Importantly, the histological evaluation of rat liver demonstrated that osthole dramatically decreased lipid accumulation (P<0.01). Conclusion:Osthole was found to have therapeutic effects on fatty milk-induced rat fatty liver; the mechanisms might be associated with its anti-oxidation and the elevation of the activities of LPL and HL.
Occurrence of Virulence Genes Associated with Diarrheagenic Pathotypes in Escherichia coli Isolates from Surface Water

ABSTRACT Escherichia coli isolates (n = 300) collected from six sites in subtropical Brisbane, Australia, prior to and after storm events were tested for the presence of 11 virulence genes (VGs) specific to diarrheagenic pathotypes. The presence of eaeA, stx 1, stx 2, and ehxA genes specific for the enterohemorrhagic E. coli (EHEC) pathotype was detected in 56%, 6%, 10%, and 13% of isolates, respectively. The VGs astA (69%) and aggR (29%), carried by enteroaggregative (EAEC) pathotypes, were frequently detected in E. coli isolates. The enteropathogenic E. coli (EPEC) gene bfp was detected in 24% of isolates. In addition, enteroinvasive E. coli (EIEC) VG ipaH was also detected in 14% of isolates. During dry periods, isolates belonging to the EAEC pathotype were most commonly detected (23%), followed by EHEC (11%) and EPEC (11%). Conversely, a more uniform prevalence of pathotypes, EPEC (14%), EAEC (12%), EIEC (10%), EHEC (7%), and ETEC (7%), was observed after the storm events. The results of this study highlight the widespread occurrence of potentially diarrheagenic pathotypes in the urban aquatic ecosystems. While the presence of VGs in E. coli isolates alone is insufficient to determine pathogenicity, the presence of diarrheagenic E. coli pathotypes in high frequency after the storm events could lead to increased health risks if untreated storm water were to be used for nonpotable purposes and recreational activities.
Effects of the US monetary policy shocks during financial crises – a threshold vector autoregression approach

ABSTRACT This article analyzes the impact of monetary policy during periods of low and high financial stress in the US economy using a threshold vector autoregression model. There is evidence that expansionary monetary policy is effective during periods of high financial stress with larger responses having a higher proportionate effect on output. The existence of a cost channel effect during periods of high financial stress implies the existence of a short run output-inflation trade off during financial crises. Large expansionary monetary shocks also increase the likelihood of moving the economy out of a high financial stress regime.
Stability preserving post-processing methods applied in the Loewner framework

We provide an overview of the Loewner methodology which is an interpolatory model order reduction technique. It uses measured or computed data (e.g. measurements of the frequency response of a to-be approximated system) instead of the system matrices, and constructs reduced models based on a rank revealing factorization of appropriately constructed matrices. In some cases the resulting reduced systems may not be stable. This issue is addressed by developing reliable and robust post processing methods to yield a stable reduced model.
mTORC1 promotes survival through translational control of Mcl-1

Activation of the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway is a frequent occurrence in human cancers and a major promoter of chemotherapeutic resistance. Inhibition of one downstream target in this pathway, mTORC1, has shown potential to improve chemosensitivity. However, the mechanisms and genetic modifications that confer sensitivity to mTORC1 inhibitors remain unclear. Here, we demonstrate that loss of TSC2 in the Eμ-myc murine lymphoma model leads to mTORC1 activation and accelerated oncogenesis caused by a defective apoptotic program despite compromised AKT phosphorylation. Tumors from Tsc2+/−Eμ-Myc mice underwent rapid apoptosis upon blockade of mTORC1 by rapamycin. We identified myeloid cell leukemia sequence 1 (Mcl-1), a bcl-2 like family member, as a translationally regulated genetic determinant of mTORC1-dependent survival. Our results indicate that the extent by which rapamycin can modulate expression of Mcl-1 is an important feature of the rapamycin response.
Excellent Outcome of Immunomodulation or Bruton’s Tyrosine Kinase Inhibition in Highly Refractory Primary Cutaneous Diffuse Large B-Cell Lymphoma, Leg Type

Primary cutaneous diffuse large B-cell lymphoma, leg type (PCDLBCL-LT) is a rare diffuse large B-cell lymphoma confined to the skin of the legs. The typical presentation is characterized by solitary or multiple growing plaques, usually confined to one leg. We report a case of PCDLBCL-LT of activated B-cell subtype characterized by multiple local relapses in the legs, initially, and systemic relapses about seven years after the diagnosis. Local relapses were sensitive to radiation therapy. Cutaneous and systemic relapses responded well to immunomodulatory therapy with lenalidomide followed by Bruton’s tyrosine kinase inhibition with ibrutinib. Ibrutinib is the only treatment that resulted in long-lasting complete remission. Lenalidomide and especially ibrutinib appear to have a significant activity against this lymphoma and should be incorporated in the treatment of this resistant and aggressive lymphoma. To our knowledge, this is the first case of PCDLBCL-LT reported in the literature exhibiting a complete response to ibrutinib.
Participation of hypothalamic CB1 receptors in reproductive axis disruption during immune challenge

Immune challenge inhibits reproductive function and endocannabinoids (eCB) modulate sexual hormones. However, no studies have been performed to assess whether the eCB system mediates the inhibition of hormones that control reproduction as a result of immune system activation during systemic infections. For that reason, we evaluated the participation of the hypothalamic cannabinoid receptor CB1 on the hypothalamic‐pituitary‐gonadal (HPG) axis activity in rats submitted to immune challenge. Male adult rats were treated i.c. v. administration with a CB1 antagonist/inverse agonist (AM251) (500 ng/5 μL), followed by an i.p. injection of lipopolysaccharide (LPS) (5 mg/kg) 15 minutes later. Plasmatic, hypothalamic and adenohypophyseal pro‐inflammatory cytokines, hormones and neuropeptides were assessed 90 or 180 minutes post‐LPS. The plasma concentration of tumour necrosis factor α and adenohypophyseal mRNA expression of Tnfα and Il1β increased 90 and 180 minutes post i.p. administration of LPS. However, cytokine mRNA expression in the hypothalamus increased only 180 minutes post‐LPS, suggesting an inflammatory delay in this organ. CB1 receptor blockade with AM251 increased LPS inflammatory effects, particularly in the hypothalamus. LPS also inhibited the HPG axis by decreasing gonadotrophin‐releasing hormone hypothalamic content and plasma levels of luteinising hormone and testosterone. These disruptor effects were accompanied by decreased hypothalamic Kiss1 mRNA expression and prostaglandin E2 content, as well as by increased gonadotrophin‐inhibitory hormone (Rfrp3) mRNA expression. All these disruptive effects were prevented by the presence of AM251. In summary, our results suggest that, in male rats, eCB mediate immune challenge‐inhibitory effects on reproductive axis at least partially via hypothalamic CB1 activation. In addition, this receptor also participates in homeostasis recovery by modulating the inflammatory process taking place after LPS administration.
Electrooptic phased array transmitter

An optically controlled transmit phased array was designed and a four-element linear array was built using integrated optics for beamforming and fiber optics for flexible remoting of the antenna. Electrooptic phase shifters remote from the antenna allowed simple electronic control of beam pointing. This phased array transmitter operated at 10 GHz with an effective isotropic radiated power (EIRP) of 14 dBW. The radiated power corresponded to approximately 0.4 W per element. The transmitted beam was electronically steered to any angle between -30/spl deg/ and 30/spl deg/ in less than 5 /spl mu/s. The measured antenna patterns agreed well with theory.
Use of Estrogen-Containing Contraception Is Associated With Increased Concentrations of 25-Hydroxy Vitamin D.

CONTEXT Small studies suggest exogenous estrogen may improve vitamin D status, but the etiology is unclear because women who use hormones may make lifestyle choices that differentially affect vitamin D status. OBJECTIVE Our objective was to investigate the association between use of hormonal contraception and 25-hydroxy-vitamin D (25(OH)D). DESIGN We used linear regression modeling of cross-sectional data to estimate percent change in season-adjusted serum 25(OH)D with estrogen use after adjustment for other factors. SETTING At the enrollment clinic visit (2010-2012) into a cohort study of uterine fibroids, each subject provided a blood sample, had anthropomorphic variables and skin reflectance measured, and answered questionnaires on demographics, dietary and supplement intake, contraceptive use, reproductive and medical history, and behaviors. PARTICIPANTS A total of 1662 African American women, community volunteers, 23-34 years old, living in the Detroit, Michigan, area were included. INTERVENTIONS None. MAIN OUTCOMES AND MEASURES Serum 25(OH)D was measured. RESULTS Serum 25(OH)D concentrations were low (70% <20 ng/ml). Current use of an estrogen-containing contraceptive was associated with a 20% (95% confidence interval: 14-27) increase in 25(OH)D after adjustment. There was no increase in 25(OH)D among participants who had used estrogen in the past, but were not current users, indicating that results were unlikely to be due to unmeasured confounding by factors related to contraceptive choice. CONCLUSIONS The increase in 25(OH)D with use of estrogen-containing contraceptives raise mechanistic questions regarding the biological pathways involved, and highlights the need for studies that examine possible endogenous estrogen effects on vitamin D.