Miracle-dz/UniFAR-FTUs huggingface dataset:
Cholinergic innervation of the cerebellum of rat, rabbit, cat, and monkey as revealed by choline acetyltransferase activity and immunohistochemistry

The cholinergic innervation of the cerebellar cortex of the rat, rabbit, cat and monkey was studied by immunohistochemical localization of choline acetyltransferase (ChAT) and radiochemical measurement of regional differences in ChAT activity. Four antibodies to ChAT were used to find optimal immunohistochemical localization of this enzyme. These antibodies selectively labeled large mossy fiber rosettes as well as finely beaded terminals with different morphological characterization, laminar distribution within the cerebellar cortex, and regional differences within the cerebellum.
Improving HomePlug Power Line Communications with LDPC Coded OFDM

Power line communications (PLC) has received much attention due to the wide connectivity and availability of power lines. Effective PLC must overcome the harsh and noisy environments inherent in PLC channels. HomePlug 1.0 is the current PLC standard in North America. The physical layer of HomePlug 1.0 employs orthogonal frequency division multiplexing (OFDM) as well as concatenated Reed-Solomon and convolutional coding. Aiming to obtain higher PLC throughput, we investigate the performance of OFDM with low-density parity-check (LDPC) codes and compare the proposed scheme with HomePlug 1.0 ROBO mode. In our simulations, the PLC channel is modeled by multipath fading, with Middleton's Class A noise (AWCN) model simulating the worst-case impulsive noise. We apply clipping to lessen the impact of impulsive noise. A simple but effective method is devised to estimate the variance of the clipped noise for LDPC decoding. In comparison with ROBO mode, the proposed scheme offers improved performance and lower computational complexity per decoded bit. Our scheme provides increased throughput by dispensing with ROBO mode's repetitive transmission of information to gain time diversity
Primary pulmonary lymphoma

Three distinct entities are now covered by the definition of primary pulmonary clonal lymphoid proliferation. The aim of this review is to describe the pathophysiological, diagnostic, prognostic and therapeutic aspects of these three entities. Low-grade pulmonary B-cell lymphoma is the most frequent form of primary pulmonary clonal lymphoid proliferation. It arises from mucosa-associated lymphoid tissue. It is usually indolent and appears in the form of a chronic alveolar opacity. The prognosis is excellent, but treatment is controversial (simple monitoring, surgery or single-agent chemotherapy). High-grade pulmonary B-cell lymphoma is far rarer and usually occurs in individuals with an underlying disorder (e.g. immunodeficiency). The prognosis is poor and therapeutic options depend on the underlying disorder. The inclusion of lymphomatoid granulomatosis in the definition of primary pulmonary lymphomas is controversial. The clonal nature of the proliferation is very rarely demonstrated and extrapulmonary involvement is frequent (upper airways, skin, kidneys, central nervous system, etc.). The prognosis is extremely variable, with some authors reporting complete remission with steroids and cyclophosphamide and others reporting failure of combination chemotherapy.
SHEF-MIME: Word-level Quality Estimation Using Imitation Learning

We describe University of Shefﬁeld’s sub-mission to the word-level Quality Estimation shared task. Our system is based on imitation learning, an approach to structured prediction which relies on a classiﬁer trained on data generated appropriately to ameliorate error propagation. Compared to other structure prediction approaches such as conditional random ﬁelds, it allows the use of arbitrary information from previous tag predictions and the use of non-decomposable loss functions over the structure. We explore these two aspects in our submission while using the baseline features provided by the shared task organ-isers. Our system outperformed the conditional random ﬁeld baseline while using the same feature set.
Brachyspira hyodysenteriae and B. pilosicoli Proteins Recognized by Sera of Challenged Pigs

The spirochetes Brachyspira hyodysenteriae and B. pilosicoli are pig intestinal pathogens that are the causative agents of swine dysentery (SD) and porcine intestinal spirochaetosis (PIS), respectively. Although some inactivated bacterin and recombinant vaccines have been explored as prophylactic treatments against these species, no effective vaccine is yet available. Immunoproteomics approaches hold the potential for the identification of new, suitable candidates for subunit vaccines against SD and PIS. These strategies take into account the gene products actually expressed and present in the cells, and thus susceptible of being targets of immune recognition. In this context, we have analyzed the immunogenic pattern of two B. pilosicoli porcine isolates (the Spanish farm isolate OLA9 and the commercial P43/6/78 strain) and one B. hyodysenteriae isolate (the Spanish farm V1). The proteins from the Brachyspira lysates were fractionated by preparative isoelectric focusing, and the fractions were analyzed by Western blot with hyperimmune sera from challenged pigs. Of the 28 challenge-specific immunoreactive bands detected, 21 were identified as single proteins by MS, while the other 7 were shown to contain several major proteins. None of these proteins were detected in the control immunoreactive bands. The proteins identified included 11 from B. hyodysenteriae and 28 from the two B. pilosicoli strains. Eight proteins were common to the B. pilosicoli strains (i.e., elongation factor G, aspartyl-tRNA synthase, biotin lipoyl, TmpB outer membrane protein, flagellar protein FlaA, enolase, PEPCK, and VspD), and enolase and PEPCK were common to both species. Many of the identified proteins were flagellar proteins or predicted to be located on the cell surface and some of them had been previously described as antigenic or as bacterial virulence factors. Here we report on the identification and semiquantitative data of these immunoreactive proteins which constitute a unique antigen collection from these bacteria.
The compensatory dynamic of inter-hemispheric interactions in visuospatial attention revealed using rTMS and fMRI

A balance of mutual tonic inhibition between bi-hemispheric posterior parietal cortices is believed to play an important role in bilateral visual attention. However, experimental support for this notion has been mainly drawn from clinical models of unilateral damage. We have previously shown that low-frequency repetitive TMS (rTMS) over the intraparietal sulcus (IPS) generates a contralateral attentional deficit in bilateral visual tracking. Here, we used functional magnetic resonance imaging (fMRI) to study whether rTMS temporarily disrupts the inter-hemispheric balance between bilateral IPS in visual attention. Following application of 1 Hz rTMS over the left IPS, subjects performed a bilateral visual tracking task while their brain activity was recorded using fMRI. Behaviorally, tracking accuracy was reduced immediately following rTMS. Areas ventro-lateral to left IPS, including inferior parietal lobule (IPL), lateral IPS (LIPS), and middle occipital gyrus (MoG), showed decreased activity following rTMS, while dorsomedial areas, such as Superior Parietal Lobule (SPL), Superior occipital gyrus (SoG), and lingual gyrus, as well as middle temporal areas (MT+), showed higher activity. The brain activity of the homologues of these regions in the un-stimulated, right hemisphere was reversed. Interestingly, the evolution of network-wide activation related to attentional behavior following rTMS showed that activation of most occipital synergists adaptively compensated for contralateral and ipsilateral decrement after rTMS, while activation of parietal synergists, and SoG remained competing. This pattern of ipsilateral and contralateral activations empirically supports the hypothesized loss of inter-hemispheric balance that underlies clinical manifestation of visual attentional extinction.
Detection of Listeria monocytogenes by using the polymerase chain reaction

A method was developed for detection of Listeria monocytogenes by polymerase chain reaction amplification followed by agarose gel electrophoresis or dot blot analysis with a 32P-labeled internal probe. The technique identified 95 of 95 L. monocytogenes strains, 0 of 12 Listeria strains of other species, and 0 of 12 non-Listeria strains.
Probabilistic independent component analysis for functional magnetic resonance imaging

We present an integrated approach to probabilistic independent component analysis (ICA) for functional MRI (FMRI) data that allows for nonsquare mixing in the presence of Gaussian noise. In order to avoid overfitting, we employ objective estimation of the amount of Gaussian noise through Bayesian analysis of the true dimensionality of the data, i.e., the number of activation and non-Gaussian noise sources. This enables us to carry out probabilistic modeling and achieves an asymptotically unique decomposition of the data. It reduces problems of interpretation, as each final independent component is now much more likely to be due to only one physical or physiological process. We also describe other improvements to standard ICA, such as temporal prewhitening and variance normalization of timeseries, the latter being particularly useful in the context of dimensionality reduction when weak activation is present. We discuss the use of prior information about the spatiotemporal nature of the source processes, and an alternative-hypothesis testing approach for inference, using Gaussian mixture models. The performance of our approach is illustrated and evaluated on real and artificial FMRI data, and compared to the spatio-temporal accuracy of results obtained from classical ICA and GLM analyses.
Using a user-level memory thread for correlation prefetching

This paper introduces the idea of using a user-level memory thread (ULMT) for correlation prefetching. In this approach, a user thread runs on a general-purpose processor in main memory, either in the memory controller chip or in a DRAM chip. The thread performs correlation prefetching in software, sending the prefetched data into the L2 cache of the main processor. This approach requires minimal hardware beyond the memory processor: the correlation table is a software data structure that resides in the main memory, while the main processor only needs a few modifications to its L2 cache so that it can accept incoming prefetches. In addition, the approach has wide usability, as it can effectively prefetch even for irregular applications. Finally, it is very flexible, as the prefetching algorithm can be customized by the user on an application basis. Our simulation results show that, through a new design of the correlation table and prefetching algorithm, our scheme delivers good results. Specifically, nine mostly-irregular applications show an average speedup of 1.32. Furthermore, our scheme works well in combination with a conventional processor-side sequential prefetcher, in which case the average speedup increases to 1.46. Finally, by exploiting the customization of the prefetching algorithm, we increase the average speed up to 1.53.
Implicit Space-Time Domain Decomposition Methods for Stochastic Parabolic Partial Differential Equations

We introduce and study parallel space-time domain decomposition methods for solving deterministic and stochastic parabolic equations. Traditional parallel algorithms solve parabolic problems time step by time step. The parallelism is restricted to each time step, and the algorithms are purely sequential in time. In this paper, we develop some overlapping Schwarz methods whose subdomains cover both space and time variables, and we show that the methods work well for stochastic parabolic equations discretized with an implicit stochastic Galerkin method. One- and two-level Schwarz preconditioned recycling GMRES methods are carefully investigated such that many components of the methods are reused when a large number of linear systems are solved. The key elements of this approach include an ordering algorithm and two grouping algorithms. We present some experimental results obtained on a parallel computer with more than one thousand processors.
Toxicity of Antiviral Nucleoside Analogs and the Human Mitochondrial DNA Polymerase*

To examine the role of the mitochondrial polymerase (Pol γ) in clinically observed toxicity of nucleoside analogs used to treat AIDS, we examined the kinetics of incorporation catalyzed by Pol γ for each Food and Drug Administration-approved analog plus 1-(2-deoxy-2-fluoro-β-d-arabinofuranosyl)-5-iodouracil (FIAU), β-L-(−)-2′,3′-dideoxy-3′-thiacytidine (−)3TC, and (R)-9-(2-phosphonylmethoxypropyl)adenine (PMPA). We used recombinant exonuclease-deficient (E200A), reconstituted human Pol γ holoenzyme in single turnover kinetic studies to measureK d (K m ) andk pol (k cat) to estimate the specificity constant (k cat/K m ) for each nucleoside analog triphosphate. The specificity constants vary more than 500,000-fold for the series ddC > ddA (ddI) > 2′,3′-didehydro-2′,3′-dideoxythymidine (d4T) ≫ (+)3TC ≫ (−)3TC > PMPA > azidothymidine (AZT) ≫ Carbovir (CBV). Abacavir (prodrug of CBV) and PMPA are two new drugs that are expected to be least toxic. Notably, the higher toxicities of d4T, ddC, and ddA arose from their 13–36-fold tighter binding relative to the normal dNTP even though their rates of incorporation were comparable with PMPA and AZT. We also examined the rate of exonuclease removal of each analog after incorporation. The rates varied from 0.06 to 0.0004 s−1 for the series FIAU > (+)3TC ∼ (−)3TC > CBV > AZT > PMPA ∼ d4T ≫ ddA (ddI) ≫ ddC. Removal of ddC was too slow to measure (<0.00002 s−1). The high toxicity of dideoxy compounds, ddC and ddI (metabolized to ddA), may be a combination of high rates of incorporation and ineffective exonuclease removal. Conversely, the more effective excision of (−)3TC, CBV, and AZT may contribute to lower toxicity. FIAU is readily extended by the next correct base pair (0.13 s−1) faster than it is removed (0.06 s−1) and, therefore, is stably incorporated and highly mutagenic. We define a toxicity index for chain terminators to account for relative rates of incorporation versus removal. These results provide a method to rapidly screen new analogs for potential toxicity.
Evaluation of RGS4 as a candidate gene for schizophrenia

Several studies have suggested that the regulator of G‐protein signaling 4 (RGS4) may be a positional and functional candidate gene for schizophrenia. Three single nucleotide polymorphisms (SNP) located at the promoter region (SNP4 and SNP7) and the intron 1 (SNP18) of RGS4 have been verified in different ethnic groups. Positive results have been reported in these SNPs with different numbers of SNP combinatory haplotypes. In this study, these three SNP markers were genotyped in 218 schizophrenia pedigrees of Taiwan (864 individuals) for association analysis. Among these three SNPs, neither SNP4, SNP7, SNP18 has shown significant association with schizophrenia in single locus association analysis, nor any compositions of the three SNP haplotypes has shown significantly associations with the DSM‐IV diagnosed schizophrenia. Our results fail to support the RGS4 as a candidate gene for schizophrenia when evaluated from these three SNP markers. © 2006 Wiley‐Liss, Inc.
Protective efficacy of protein A-specific antibody against bacteremic infection due to Staphylococcus aureus in an infant rat model

Staphylococcal protein A (SpA) is a potent antiphagocytic component of the cell wall of most pathogenic Staphylococcus aureus strains. We studied the in vitro opsonophagocytic and in vivo protective activities of rabbit immunoglobulin G (IgG) antibody to purified SpA obtained from two unencapsulated S. aureus strains (Cowan I and 17A). Postimmune serum contained high titers of specific IgG to SpA, as measured by a modified enzyme-linked immunosorbent assay that blocked nonspecific binding of IgG to SpA. In vitro, both S. aureus strains were efficiently phagocytosed and killed by polymorphonuclear leukocytes in the presence of nonimmune sera and complement. With one strain (Cowan I), opsonophagocytosis was significantly enhanced in the presence of SpA antibody, but with the other strain (17A), killing was significantly decreased with immune serum. We then evaluated the potential protective benefit of SpA antibody in preventing S. aureus bacteremia in infant rats. Two-day-old rats received saline or various doses of SpA antiserum and were challenged subcutaneously 1 day later, but even the highest levels of antibody did not significantly reduce mortality, bacteremia or metastatic infection to lungs or liver (frequency or magnitude). This lack of protective efficacy was not related to a failure of SpA F(ab')2 to bind to cell surface-exposed epitopes, since F(ab')2 fragments prepared from hyperimmune serum bound avidly to the whole organism in an enzyme-linked immunosorbent assay.
Pathology and Pathobiology of Pulmonary Hypertension

Abstract Pulmonary hypertension is a devastating, life-threatening disorder with no curative options, characterized by elevated pulmonary vascular resistance and secondary right ventricular failure. Although the etiologies of pulmonary arterial hypertension are multiple and its pathogenesis is complex, there is growing evidence that inflammation, endothelial dysfunction, aberrant vascular wall cell proliferation, as well as mutations in the bone morphogenetic protein receptor type 2 gene play a crucial role in triggering pathological vascular remodeling. The present article outlines the current understanding of this disease from the point of view of pathology and pathobiology.
Multidecadal trends in area burned with high severity in the Selway-Bitterroot Wilderness Area 1880–2012

Multidecadal trends in areas burned with high severity shape ecological effects of fires, but most assessments are limited to ~30 years of satellite data. We analysed the proportion of area burned with high severity, the annual area burned with high severity, the probability areas burned with high severity and also the area reburned (all severities and high burn severity only) over 133 years across 346265ha within the Selway-Bitterroot Wilderness (SBW) Area in Idaho, United States. We used burn severity class inferred from digitised aerial photography (1880–2000) and satellite imagery (1973–2012). Over this long record, the proportion burned with high severity did not increase, despite extensive area burned in recent decades. Much greater area burned with high severity during the Early (1880–1934) and Late (1975–2012) periods than during the Middle period (1935–1974), paralleling trends in area burned. Little area reburned with high severity, and fires in the Early period limited the extent of fires burning decades later in the Late period. Our results suggest that long-term data across large areas provides useful context on recent trends, and that projections for the extent and severity of future fires must consider prior fires and fire management.
The Role of Kv7/M Potassium Channels in Controlling Ectopic Firing in Nociceptors

Peripheral nociceptive neurons encode and convey injury-inducing stimuli toward the central nervous system. In normal conditions, tight control of nociceptive resting potential prevents their spontaneous activation. However, in many pathological conditions the control of membrane potential is disrupted, leading to ectopic, stimulus-unrelated firing of nociceptive neurons, which is correlated to spontaneous pain. We have investigated the role of KV7/M channels in stabilizing membrane potential and impeding spontaneous firing of nociceptive neurons. These channels generate low voltage-activating, noninactivating M-type K+ currents (M-current, IM), which control neuronal excitability. Using perforated-patch recordings from cultured, rat nociceptor-like dorsal root ganglion neurons, we show that inhibition of M-current leads to depolarization of nociceptive neurons and generation of repetitive firing. To assess to what extent the M-current, acting at the nociceptive terminals, is able to stabilize terminals' membrane potential, thus preventing their ectopic activation, in normal and pathological conditions, we built a multi-compartment computational model of a pseudo-unipolar unmyelinated nociceptive neuron with a realistic terminal tree. The modeled terminal tree was based on the in vivo structure of nociceptive peripheral terminal, which we assessed by in vivo multiphoton imaging of GFP-expressing nociceptive neuronal terminals innervating mice hind paw. By modifying the conductance of the KV7/M channels at the modeled terminal tree (terminal gKV7/M) we have found that 40% of the terminal gKV7/M conductance is sufficient to prevent spontaneous firing, while ~75% of terminal gKV7/M is sufficient to inhibit stimulus induced activation of nociceptive neurons. Moreover, we showed that terminal M-current reduces susceptibility of nociceptive neurons to a small fluctuations of membrane potentials. Furthermore, we simulated how the interaction between terminal persistent sodium current and M-current affects the excitability of the neurons. We demonstrated that terminal M-current in nociceptive neurons impeded spontaneous firing even when terminal Na(V)1.9 channels conductance was substantially increased. On the other hand, when terminal gKV7/M was decreased, nociceptive neurons fire spontaneously after slight increase in terminal Na(V)1.9 conductance. Our results emphasize the pivotal role of M-current in stabilizing membrane potential and hereby in controlling nociceptive spontaneous firing, in normal and pathological conditions.
Laparoscopic management of acute peritonitis

The presence of peritonitis has previously been considered to be a contraindication for the laparoscopic approach because of the theoretical risk of malignant hypercapnia and toxic shock syndrome. The aim of this retrospective study was to demonstrate that laparoscopy is feasible, safe and efficient in cases of peritonitis.
Cost-effectiveness of cardiac resynchronization therapy: results from the CARE-HF trial.

Study population The study population comprised patients aged at least 18 years who had evidence of heart failure for at least 6 weeks and were New York Heart Association (NYHA) Class III or IV with a left ventricular ejection fraction of less then 35%, a left ventricular end-diastolic dimension of at least 30 mm, and a QRS interval of greater than 120 milliseconds (ms). Patients with a QRS interval between 120 and 149 ms had to also have two of the following: an aortic pre-ejection delay of greater than 140 ms, an interventricular mechanical delay of more than 40 ms, or delayed activation of the posterolateral left ventricular wall.
Uncoupling of M-phase kinase activation from the completion of S-phase by heat shock.

Chronic exposure of asynchronous HeLa cell cultures to 41.5 degrees C leads to an accumulation of cells in the S-phase, spontaneous premature chromosome condensation, and loss of clonogenicity (M.A. Mackey, S. L. Anolik, and J. L. Roti Roti. Cancer Res., 52: 1101-1106, 1992). In this report, we show that increases in histone H1 kinase activity during 41.5 degrees C exposure occur coincidentally with the appearance of premature chromosome condensation. Furthermore, this kinase activity is shown to be associated with M-phase kinase complexes containing cyclin B1. These increases in the activity of M-phase kinase were found to occur concomitantly with an elevation in cyclin B1 mRNA and an accumulation of cyclin B1 protein. Because cyclin B1 transcription begins in the S-phase, it is probable that the heat-induced delay in the S-phase allows the accumulation of abnormally high cyclin B1 levels. Elevated cyclin B1 levels could then account for the observed abrogation of the cell cycle checkpoint, which usually assures that mitosis does not proceed until DNA replication is complete. This involvement of M-phase kinase in heat-induced cytotoxicity demonstrates the importance of the coordinate regulation of the processes of DNA replication and entry into mitosis.