Miracle-dz/UniFAR-FTUs huggingface dataset:
An Approach to Parallel M × N Communication

High performance scientific applications are frequently multiphysics codes composed from single-physics programs, or have a functional decomposition based on physics as well as a domain decomposition for parallelism. In either case, dividing the application into independent components that can be developed and tested separately is useful. This requires a fast and efficient mechanism to share the large parallel data structures that are used in scientific applications. The “ M× Nproblem” is the transfer of data between two scientific parallel programs with different numbers of processes on each side. We present a solution to the M× Nproblem based on an I/O message passing interface (MPI). In this solution, the client application reads and writes data using the standard MPI I/O, but instead of going to hard drives the data are streamed in parallel between module programs working together on an integrated simulation. This approach builds on existing technology, emphasizes the easy migration of current applications, and simplifies the unit testing of the components while maintaining parallel high performance throughout the application. It also does not require a component to know how many processes another communicating component has.
Sequential and Synchronous Chemo-Radiotherapy in the Management of Locally Advanced Carcinoma of the Head and Neck

Thirty-nine consecutive patients with stage III-IV squamous cell carcinoma of the head and neck entered a pilot study of sequential and synchronous chemo-radiotherapy. The study was planned as follows: two cycles of induction chemotherapy (MTX, BLM, DDP) followed by radical radiotherapy (66 Gy) with synchronous weekly administration of DDP (20 mg/m2) as a radiosensitizer. Out of the 39 patients evaluable for induction chemotherapy 25 (64%) achieved partial or complete response. Two patients underwent radical surgery after induction chemotherapy and 3 patients died of treatment. Out of the remaining 34 patients, 25 were untreated and 9 presented recurrence after primary surgery. Grade 4 mucositis was the major side effect of concurrent chemo-radiotherapy. Local control after synchronous therapy was obtained In 11 (44%) previously untreated patients and only in 1 (11%) patient of the surgically pretreated group. At the time of the analysis 11 patients were alive, 8 of them free from disease (4 after salvage surgery). Actuarial 2-year survival for previously untreated patients was 33% and 24% for all the patients. This survival is not significantly different (log rank test) from that of a similar group of 24 patients treated at the same institution with radiotherapy alone. The important toxicity of the induction chemotherapy regimen and the poor 2-year survival do not show any benefit from such a combined approach in locally advanced head and neck carcinoma. Nevertheless, despite our disappointing results many data in the literature suggest a role for chemotherapy-based treatments of locally advanced head and neck cancer. Further controlled randomized studies are required to better define the place of chemotherapy in the multi-modality management of stage III-IV head and neck cancer.
Interactive comment on “ Miniaturized biosignature analysis reveals implications for the formation of cold seep carbonates at Hydrate Ridge ( off Oregon , USA ) ” by T . Leefmann et al .

Methane-related carbonates from Hydrate Ridge typically show several macroscopically distinguishable mineral phases, namely whitish aragonite, lucent aragonite, and gray micrite. The relationship of these phases to particular microorganisms or biogeochemical processes is as yet unclear. We used a miniaturized biomarker technique on mg samples, combined with factor analysis and subsequent electron microprobe analysis, to study lipid biomarkers and chemical compositions of the individual phases. This allows us to identify particular mechanisms involved in the formation of the different carbonate precipitates. Our combined analysis of biomarkers and petrographic traits shows that most of the lipids related to the anaerobic oxidation of methane ( >90% by weight) are concentrated within only a minor compartment ( ∼20% by volume) of the Hydrate Ridge carbonates, the whitish aragonite. The patterns indicate that the whitish aragonite represents fossilized biofilms of methanotrophic consortia containing mainly archaea of the ANME-2 group and sulfate reducing bacteria, whereas the precipitation of the lucent aragonite may have lacked the immediate proximity of microorganisms during formation. By contrast, the gray micrite formed by incorporation of allochthonous organic and inorganic matter during carbonate precipitation induced by the anaerobic oxidation of methane involving ANME-1 archaea. Correspondence to: V. Thiel (vthiel@gwdg.de)
Recovery of Sparsely Corrupted Signals

We investigate the recovery of signals exhibiting a sparse representation in a general (i.e., possibly redundant or incomplete) dictionary that are corrupted by additive noise admitting a sparse representation in another general dictionary. This setup covers a wide range of applications, such as image inpainting, super-resolution, signal separation, and recovery of signals that are impaired by, e.g., clipping, impulse noise, or narrowband interference. We present deterministic recovery guarantees based on a novel uncertainty relation for pairs of general dictionaries and we provide corresponding practicable recovery algorithms. The recovery guarantees we find depend on the signal and noise sparsity levels, on the coherence parameters of the involved dictionaries, and on the amount of prior knowledge about the signal and noise support sets.
Proliferation pattern of capillary endothelial cells in chorioallantoic membrane development indicates local growth control, which is counteracted by vascular endothelial growth factor application

The density and distribution of whole mount BrdU‐anti‐BrdU labeled endothelial cells (days 6–15) in the chick chorioallantoic membrane (CAM) was analyzed with computer‐assisted microscopy. A significant loss of proliferative activity was noted after day 10: the density of labeled nuclei (in 10−2 mm−2) decreased from a median 7.78 (days 6, 8, 10) to 2.42 (days 12, 14, 15). CAMs initially showed random patterns of labeled endothelial cells, but changed to clearly focal patterns after day 12. A regular arrangement of labeled nuclei was never seen. After application of vascular endothelial growth factor (VEGF) to the day 13 CAM, a significant increase in proliferative activity (11.50) and a random distribution of labeled endothelial cells was observed on day 15. Development of CAM precapillary vessels was assessed in terms of length density (in mm−1, mean ± standard deviation), which was augmented threefold from day 6 (1.22 ± 0.05) to day 14 (3.54 ± 0.23) and then remained nearly constant. VEGF application from day 13 to 15 raised arterial length per unit area to 4.53 ± 0.77. It is concluded that normally a local regulation of endothelial proliferation and differentiation develops in the CAM, which doubles capillary endothelial cell density but simultaneously adapts to the decreasing need for endothelial cells, and thus maintains the quasi two‐dimensional vessel pattern. However, proliferative foci persist in the capillary layer after day 10, and precapillary vessel density continues to increase until day 14. VEGF enhances DNA synthesis in all capillary endothelial cells. This leads to the disappearance of proliferative foci, to multiple capillary layers, and to an excessive formation of precapillary vessels. We propose that CAM endothelial cell proliferation is regulated by factors like endothelial cell density and extension. The proliferative pattern in capillaries, and the length density of precapillary vessels should be used for the evaluation of angiogenesis in the CAM assay. We recommend the CAM after day 12 for evaluating putative angiogenic mitogens. ©1995 Wiley‐Liss, Inc.
A comparative approach to testing hypotheses for the evolution of sex‐biased dispersal in bean beetles

Abstract Understanding the selective forces that shape dispersal strategies is a fundamental goal of evolutionary ecology and is increasingly important in changing, human‐altered environments. Sex‐biased dispersal (SBD) is common in dioecious taxa, and understanding variation in the direction and magnitude of SBD across taxa has been a persistent challenge. We took a comparative, laboratory‐based approach using 16 groups (species or strains) of bean beetles (genera Acanthoscelides, Callosobruchus, and Zabrotes, including 10 strains of one species) to test two predictions that emerge from dominant hypotheses for the evolution of SBD: (1) groups that suffer greater costs of inbreeding should exhibit greater SBD in favor of either sex (inbreeding avoidance hypothesis) and (2) groups with stronger local mate competition should exhibit greater male bias in dispersal (kin competition avoidance hypothesis). We used laboratory experiments to quantify SBD in crawling dispersal, the fitness effects of inbreeding, and the degree of polygyny (number of female mates per male), a proxy for local mate competition. While we found that both polygyny and male‐biased dispersal were common across bean beetle groups, consistent with the kin competition avoidance hypothesis, quantitative relationships between trait values did not support the predictions. Across groups, there was no significant association between SBD and effects of inbreeding nor SBD and degree of polygyny, using either raw values or phylogenetically independent contrasts. We discuss possible limitations of our experimental approach for detecting the predicted relationships, as well as reasons why single‐factor hypotheses may be too simplistic to explain the evolution of SBD.
Macroscopic hematuria as a presentation of gestational trophoblastic neoplasia in an adolescent woman

Gestational trophoblastic neoplasia (GTN) is a hemorrhagic malignancy with highly rapid potential metastasis via hematogenous spreading. Renal metastasis is of infrequent occurrence. Among previous case reports of renal metastasis in GTN, this is the youngest woman presenting a large renal lesion concurrent with pulmonary and brain metastases. Disease remission had been achieved by treatment with combined chemotherapy and whole brain radiation, although acute myeloblastic leukemia (AML) developed later.
Variables Related to Undergraduate Students Preference for Distance Education Classes.

The purpose of this research is to identify student-specific characteristics that are related to students’ preference for distance education courses. Since distance education courses provide students with more convenient and flexible class schedules, they should be preferred by students who have a greater number of competing demands, such as work and family, on their time. Not surprisingly, previous research has shown that such competing demands are also risk factors for undergraduate degree non-completion. Therefore a major purpose of this research is to examine whether students with risk factors for noncompletion of their undergraduate degree prefer distance education courses. Another purpose of this research is to examine whether students with a disability that limits their mobility, and thus experience greater barriers to access their face-to-face class rooms, prefer distance education classes. For this research, the data are from the National Postsecondary Student Aid Survey (NPSAS) conducted in 200304. The NPSAS uses a complex survey design to collect data from a nationally representative sample of about 80,000 postsecondary undergraduate students in the US. Results confirm that students with increasing number of risk factors for non-completion of their degree show a significantly greater preference for distance education courses. Results also show that students with limited mobility also prefer distance education classes. Taken together, these results suggest that distance education classes are likely to increase enrollment and degree completion rates both for non-traditional undergraduates, who have more risk factors for degree non-completion than traditional undergraduates, and for students with physical disabilities that limit their mobility.
Cellobiose-Mediated Gene Expression in Streptococcus pneumoniae: A Repressor Function of the Novel GntR-Type Regulator BguR

The human pathogen Streptococcus pneumoniae has the ability to use the carbon- and energy source cellobiose due to the presence of a cellobiose-utilizing gene cluster (cel locus) in its genome. This system is regulated by the cellobiose-dependent transcriptional activator CelR, which has been previously shown to contribute to pneumococcal virulence. To get a broader understanding of the response of S. pneumoniae to cellobiose, we compared the pneumococcal transcriptome during growth on glucose as the main carbon source to that with cellobiose as the main carbon source. The expression of various carbon metabolic genes was altered, including a PTS operon (which we here denote as the bgu operon) that has high similarity with the cel locus. In contrast to the cel locus, the bgu operon is conserved in all sequenced strains of S. pneumoniae, indicating an important physiological function in the lifestyle of pneumococci. We next characterized the transcriptional regulation of the bgu operon in more detail. Its expression was increased in the presence of cellobiose, and decreased in the presence of glucose. A novel GntR-type transcriptional regulator (which we here denote as BguR) was shown to act as a transcriptional repressor of the bgu operon and its repressive effect was relieved in the presence of cellobiose. BguR-dependent repression was demonstrated to be mediated by a 20-bp DNA operator site (5′-AAAAATGTCTAGACAAATTT-3′) present in PbguA, as verified by promoter truncation experiments. In conclusion, we have identified a new cellobiose-responsive PTS operon, together with its transcriptional regulator in S. pneumoniae.
Gastric polypectomy.

In 138 patients of 215 gastric polyps were removed by electroresection through a fiberscope and the polyps recovered in toto by suction or special grasper-forceps. Discepancies of histological findings in the biopsy specimens and in the tissue of the whole polyps were often found. Follow-up examinations of the cases were presented. Based on our experiences a new histological classification of gastric polyps is neccessary.
The Molecular Basis of Temperature Compensation in the Arabidopsis Circadian Clock[W]

Circadian clocks maintain robust and accurate timing over a broad range of physiological temperatures, a characteristic termed temperature compensation. In Arabidopsis thaliana, ambient temperature affects the rhythmic accumulation of transcripts encoding the clock components TIMING OF CAB EXPRESSION1 (TOC1), GIGANTEA (GI), and the partially redundant genes CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY). The amplitude and peak levels increase for TOC1 and GI RNA rhythms as the temperature increases (from 17 to 27°C), whereas they decrease for LHY. However, as temperatures decrease (from 17 to 12°C), CCA1 and LHY RNA rhythms increase in amplitude and peak expression level. At 27°C, a dynamic balance between GI and LHY allows temperature compensation in wild-type plants, but circadian function is impaired in lhy and gi mutant plants. However, at 12°C, CCA1 has more effect on the buffering mechanism than LHY, as the cca1 and gi mutations impair circadian rhythms more than lhy at the lower temperature. At 17°C, GI is apparently dispensable for free-running circadian rhythms, although partial GI function can affect circadian period. Numerical simulations using the interlocking-loop model show that balancing LHY/CCA1 function against GI and other evening-expressed genes can largely account for temperature compensation in wild-type plants and the temperature-specific phenotypes of gi mutants.
Clinicopathological description of two cases with SQSTM1 gene mutation associated with frontotemporal dementia

There is a strong genetic influence on the clinicopathological phenotypes associated with frontotemporal lobar degeneration (FTLD) and frontotemporal dementia (FTD). Intracellular deposition of TDP‐43 is the phenotypical hallmark of a frequent subgroup of cases. Mutations in the sequestosome 1 (SQSTM1) gene have rarely been found in individuals with FTD. Here we provide a comprehensive clinicopathological description of two cases with a SQSTM1 mutation. The clinical phenotype of patient 1 (mutation p.Glu396*) was compatible with the behavioural variant (bv) of FTD. TDP‐43 pathology was consistent with the features of type B of FTLD‐TDP pathology. However, prominent neuronal granular cytoplasmic TDP‐43 immunoreactivity and abundant oligodendroglial inclusions, proven by colocalization with the oligodendroglial‐marker TPPP/p25, were also seen. The clinical phenotype of patient 2 was compatible with bvFTD associated with parkinsonism and bulbar symptoms in the later stage. Genetic testing of patient 2 identified a C9orf72 repeat expansion mutation together with a missense mutation (p.Arg212Cys) in SQSTM1. TDP‐43 pathology was characterized by neuritic profiles compatible mostly with type A. In contrast to patient 1, p62 pathology was seen to a greater extent as TDP‐43 immunoreactivity in neurons. Using an antibody that detects poly(GP) peptides produced via repeat associated non‐ATG translation associated with expanded hexanucleotide repeat in the C9orf72 gene, we confirmed the presence of pathognomonic inclusions. The present study supports previous observations on amyotrophic lateral sclerosis (ALS) that SQSTM1 mutations consistently associate with TDP‐43 pathology. The co‐presence of C9orf72 mutation may influence the phenotype, thus finding one FTLD (or ALS) related mutation does not exclude the presence of further influential genetic alterations. Oligodendroglial TDP‐43 pathology is considerable in some forms of FTLD‐TDP, thus their evaluation might be considered to be included in classification systems.
Toward a criterion for suspect thiouracil administration in animal husbandry

Thyreostats are growth-promoters banned in Europe since 1981. The identification of thiouracil (TU) in animal biological matrices can, however, no longer be systematically interpreted as a consequence of illegal administration. Indeed, some experimental results have indicated a causal link between cruciferous-based diet and the presence of TU in urine of bovines. The present study aims at investigating, on a large scale (n > 1300), the natural occurrence of thiouracil in urine samples collected from different animal species. TU was identified in main breeding animal species: bovine, porcine and ovine. The natural distribution of TU allowed proposing threshold values to differentiate compliant from suspect urine samples. Suggested values are 5.7 and 9.1 µg l−1 in male adult bovines (6–24 months), 3.1 and 8.1 µg l−1 in female adult bovines (6–24 months), 7.3 and 17.7 µg l−1 in calves (<6 months), 3.9 and 8.8 µg l−1 in female bovines (>24 months), and 2.9 and 4.1 µg l−1 in porcines at a 95 and 99% confidence level, respectively.
From awareness to repartee: sharing location within social groups

This paper investigates emergent practices around 'microblogging', changing and sharing status within a social group. We present results from a trial of 'Connecto', a phone based status and location sharing application that allows a group to 'tag' areas and have individuals' locations shared automatically on a mobile phone. In use the system moved beyond being an awareness tool to a way of continuing the ongoing 'story' of conversations within the group. Through sharing status and location the system supported each groups' ongoing repartee - a site for social exchange, enjoyment and friendship.
Recent advances in 3D time‐resolved contrast‐enhanced MR angiography

Contrast‐enhanced magnetic resonance angiography (CE‐MRA) was first introduced for clinical studies approximately 20 years ago. Early work provided 3–4 mm spatial resolution with acquisition times in the 30‐second range. Since that time there has been continuing effort to provide improved spatial resolution with reduced acquisition time, allowing high resolution 3D time‐resolved studies. The purpose of this work is to describe how this has been accomplished. Specific technical enablers have been: improved gradients allowing reduced repetition times, improved k‐space sampling and reconstruction methods, parallel acquisition, particularly in two directions, and improved and higher count receiver coil arrays. These have collectively made high‐resolution time‐resolved studies readily available for many anatomic regions. Depending on the application, ∼1 mm isotropic resolution is now possible with frame times of several seconds. Clinical applications of time‐resolved CE‐MRA are briefly reviewed. J. Magn. Reson. Imaging 2015;42:3–22. © 2015 Wiley Periodicals, Inc.
The role of the J domain of SV40 large T in cellular transformation.

SV40 large T antigen (TAg)-mediated transformation is dependent on binding to p53 and the retinoblastoma tumor suppressor protein (pRB) and inactivating their growth suppressive functions. Transformation minimally requires three regions of TAg: a C-terminal domain that mediates binding to p53; the LXCXE motif (residues 103-107), necessary for binding to pRB and the related proteins p107 and p130; and an N-terminal domain (residues 1-82) that contains homology to the J domain found in cellular DnaJ/Hsp40 molecular chaperone proteins. We have found that the N-terminal J domain of T Ag cooperates with the LXCXE motif to inactivate the growth suppressive functions of the pRB-related proteins.
Roles of the Kinase TAK1 in CD40-Mediated Effects on Vascular Oxidative Stress and Neointima Formation after Vascular Injury

Although TAK1 has been implicated in inflammation and oxidative stress, its roles in vascular smooth muscle cells (VSMCs) and in response to vascular injury have not been investigated. The present study aimed to investigate the role of TAK1 in modulating oxidative stress in VSMCs and its involvement in neointima formation after vascular injury. Double immunostaining reveals that vascular injury induces a robust phosphorylation of TAK1 (Thr187) in the medial VSMCs of injured arteries in wildtype mice, but this effect is blocked in CD40-deficient mice. Upregulation of TAK1 in VSMCs is functionally important, as it is critically involved in pro-oxidative and pro-inflammatory effects on VSMCs and eventual neointima formation. In vivo, pharmacological inhibition of TAK1 with 5Z-7-oxozeaenol blocked the injury-induced phosphorylation of both TAK1 (Thr187) and NF-kB/p65 (Ser536), associated with marked inhibition of superoxide production, 3-nitrotyrosine, and MCP-1 in the injured arteries. Cell culture experiments demonstrated that either siRNA knockdown or 5Z-7-oxozeaenol inhibition of TAK1 significantly attenuated NADPH oxidase activation and superoxide production induced by CD40L/CD40 stimulation. Co-immunoprecipitation experiments indicate that blockade of TAK1 disrupted the CD40L-induced complex formation of p22phox with p47phox, p67phox, or Nox4. Blockade of TAK1 also inhibited CD40L-induced NF-kB activation by modulating IKKα/β and NF-kB p65 phosphorylation and this was related to reduced expression of proinflammatory genes (IL-6, MCP-1 and ICAM-1) in VSMCs. Lastly, treatment with 5Z-7-oxozeaenol attenuated neointimal formation in wire-injured femoral arteries. Our findings demonstrate previously uncharacterized roles of TAK1 in vascular oxidative stress and the contribution to neointima formation after vascular injury.