Miracle-dz/UniFAR-FTUs huggingface dataset:
Keratin expression in anal carcinoma: an immunohistochemical study

The keratin expression of 40 frozen tissue specimens of anal carcinoma was investigated using a panel of 17 monoclonal antibodies to 14 individual keratins. The tumours were divided into three histological subgroups showing pure squamous, squamous and basaloid, or squamous and glandular differentiation. A further assessment of the tumour grade was made. The overall profile was of expression of keratins 4, 13, 17, 18 and 19 across the majority of the tumours, with the minority expressing keratins 1 and 10, and keratin 7. Dedifferentiation was associated with loss of expression of keratinocyte keratins, particularly the cornification markers keratin 1 and 10, and K6 and 16 associated with keratinocyte hyperproliferation and differentiation. This correlated with acquisition of the simple epithelial keratins 7 and 8. Compared with the tumours as a whole, well differentiated squamous tumours (the most easily identifiable histological group) showed consistent positivity for keratins 6 and 16, expressed suprabasally, while simple keratins 18 and 19 were also found. Independent of grade, mixed tumours showed more widespread positivity for simple epithelial keratins 7, 8 and 18 and loss of expression of cornification keratins 1 and 10 and K6 and 16 compared with pure squamous tumours. The relatively limited keratin profile of pure squamous tumours, predominantly consisting of keratinocyte keratins, suggests that these malignancies are less likely to originate from the region of the anal canal where the keratin profile is heterogeneous, i.e. the anal transitional zone.
Does the Stanford Health Assessment Questionnaire have potential as a monitoring tool for subjects with rheumatoid arthritis?

OBJECTIVE To assist in the interpretation of the Stanford Health Assessment Questionnaire (HAQ) score changes for individual patients with rheumatoid arthritis (RA), by determining the minimum size of score change that can confidently be considered to reflect a significant change in disability from the patient's perspective. METHOD HAQ score changes were calculated for 40 clinic patients with RA who had reported no change to health in general over two months. These were considered to reflect both inconsistencies in questionnaire completion and any true but minor changes not considered significant enough by the patients to represent a change to their health in general. HAQ score changes over one year were also calculated for 207 clinic patients with RA. RESULTS The range within which 95% of score changes would be expected to lie in the absence of significant change was estimated as ±0.48 points (±2SD of the score changes) and 80% within ±0.31 points (±1.29SD). A χ2 test showed no significant association between an HAQ score increase of >0.31 over one year and decline in health related to arthritis reported by the patient over the same period. CONCLUSION As a general guideline, an HAQ score needs to change by 0.48 points or more for 95% confidence that it reflects significant change (0.31 for 80% confidence). Although the value of HAQ as a group outcome measure is well established, this study questions the usefulness of monitoring individual HAQ scores in a clinical setting.
Bulk Comptonization spectra in blazars

We study the time-dependent spectra produced via the bulk Compton process by a cold, relativistic shell of plasma moving (and accelerating) along the jet of a blazar, scattering on external photons emitted by the accretion disc and reprocessed in the broad-line region (BLR). The bulk Comptonization of disc photons is shown to yield a spectral component contributing in the far-ultraviolet band, and would then be currently unobservable. On the contrary, the bulk Comptonization of broad-line photons may yield a significant feature in the soft X-ray band. Such a feature is time-dependent and transient, and dominates over the non-thermal continuum only when: (i) the dissipation occurs close to, but within, the BLR; and (ii) other competing processes, like the synchrotron self-Compton emission, yield a negligible flux in the X-ray band. The presence of a bulk Compton component may account for the X-ray properties of high-redshift blazars that show a flattening (and possibly a hump) in the soft X-rays, previously interpreted as due to intrinsic absorption. We discuss why the conditions leading to a detectable bulk Compton feature might be met only occasionally in high-redshift blazars, concluding that the absence of such a feature in the spectra of most blazars should not be taken as evidence against matter-dominated relativistic jets. The detection of such a component carries key information on the bulk Lorentz factor and kinetic energy associated to (cold) leptons.
Characterization of the Secreted MPT53 Antigen ofMycobacterium tuberculosis

ABSTRACT MPT53 is a secreted protein of Mycobacterium tuberculosis. Southern transfer and hybridization showed mpt53 to be conserved in the M. tuberculosis complex and to have homology with DNA fromMycobacterium avium and other nontuberculous mycobacteria. However, anti-MPT53 polyclonal antibodies detected no antigen in the culture filtrates of M. avium and other nontuberculous mycobacteria. MPT53 of M. tuberculosisinduced strong, tuberculosis-specific antibody responses in guinea pigs but induced no delayed-type hypersensitivity. Involvement in immune responses during human tuberculosis was very modest.
Genetic characterization of trh positive Vibrio spp. isolated from Norway

The thermostable direct hemolysin (TDH) and/or TDH-related hemolysin (TRH) genes are carried by most virulent Vibrio parahaemolyticus serovars. In Norway, trh+ V. parahaemolyticus constitute 4.4 and 4.5% of the total number of V. parahaemolyticus isolated from blue mussel (Mytilus edulis) and water, respectively. The trh gene is located in a region close to the gene cluster for urease production (ure). This region was characterized in V. parahaemolyticus strain TH3996 and it was found that a nickel transport operon (nik) was located between the first gene (ureR) and the rest of the ure cluster genes. The organization of the trh-ureR-nik-ure gene cluster in the Norwegian trh+ isolates was unknown. In this study, we explore the gene organization within the trh-ureR-nik-ure cluster for these isolates. PCR analyses revealed that the genes within the trh-ureR-nik-ure gene cluster of Norwegian trh+ isolates were organized in a similar fashion as reported previously for TH33996. Additionally, the phylogenetic relationship among these trh+ isolates was investigated using Multilocus Sequence Typing (MLST). Analysis by MLST or ureR-trh sequences generated two different phylogenetic trees for the same strains analyzed, suggesting that ureR-trh genes have been acquired at different times in Norwegian V. parahaemolyticus isolates. MLST results revealed that some pathogenic and non-pathogenic V. parahaemolyticus isolates in Norway appear to be highly genetically related.
UvA-DARE ( Digital Academic Repository ) Tick-host-pathogen interactions in Lyme borreliosis

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Secondary Indexing Techniques for Key-Value Stores: Two Rings To Rule Them All

Secondary indices are traditionally used in DBMS to increase the performance of queries that do not rely on the keys of the table for data reads. Many of the newer NoSQL distributed data stores, even if they provide a table-based data model such as HBase, however, do not yet have a secondary indexing feature built in. In this paper, we explore the challenges associated with indexing modern distributed table-based data stores and investigate two secondary index approaches which we have integrated within HBase. Our detailed analysis and experimental results prove the benefits of both the approaches. Further, we demonstrate that such secondary index implementation decisions cannot be made in isolation of the data distribution and that different indexing approaches can cater to different needs.
Fifty years of disconnexion syndromes and the Geschwind legacy.

‘I read a book one day and my whole life was changed…I sat at the table turning the pages, my mind barely aware that I was reading, and my whole life was changing as I read the new words on each page. ’ [From the opening paragraph of Orhan Pamuk’s Yeni Hayat (New Life), English translation by Guneli Gun]. Had Pamuk’s protagonist been a behavioural neurologist, he might have chosen similar words to describe his first encounter with Norman Geschwind’s 1965 Disconnexion Syndromes in Animals and Man (Geschwind, 1965 a , b ). His experience would not have been unique. For the past half century, this two-part monograph has remained the most influential work ever published in the discipline that came to be known as behavioural neurology (Fig. 1). Figure 1 Norman Geschwind. (With kind permission of Claudia Geschwind). The monograph covered 116 pages of text, without a single table, figure or diagram. It offered an unprecedented synthesis of disparate neurological phenomena by translating them into the idiom of neuroanatomy at a particularly pivotal time in the history of neurological sciences. On the occasion of its 50th publication anniversary, the aim of this retrospective is to summarize for the general reader some of the main ideas in Geschwind’s monograph, highlight those that inspired further discovery, mention the few that require revision or amplification, and interpret the legacy of this paper from the vantage point of contemporary neurology. A comprehensive coverage of Disconnexion Syndromes, with a focus on broader themes related to the anatomy of cognition, appeared 10 years ago on the 40th publication anniversary of this work (Catani and ffytche, 2005). The Disconnexion Syndromes revived paradigmatic single case studies published by 19th century French and German neurologists, highlighted the functional rather than topographical subdivision of the cerebral cortex, espoused a hierarchical system …
Growing-Season Temperature Change across Four Decades in an Arctic Tundra Pond

We examined temperature dynamics across a 42-year period in a low-centered tundra polygon pond on the Arctic Coastal Plain of northern Alaska to assess potential changes in thermal dynamics for ponds of this type. Using water temperature data from a pond near Barrow (now Utqiaġvik), Alaska, studied intensively during 1971 – 73 and again in 2007 – 12, we built an empirical model coupling historical air temperatures to measured pond temperatures for four summers. We then used the model to predict summer pond temperatures over a 42-year span, including 1974 – 2008, for which direct aquatic temperature records do not exist. Average pond temperatures during the growing season (1 May through 31 October) increased by 0.5˚C decade-1 or 2.2˚C over the 42-year period. Our simulations predicted the average date of spring thaw for the pond as 2 June (± 3 d), which did not change over the 42-year time period. However, average pond temperature during the first 30 days of the growing season increased from 1971 to 2012, suggesting that recently, ponds are warmer in early spring. The average date of pond sediment freeze over the 42 years shifted later by 15 days, from 28 September in 1971 to 13 October in 2012. These changes correspond to a growing season that has increased in length by 14 days, from 118 days in 1971 to 132 days in 2012. Contemporary temperature measurements in other shallow tundra ponds in northern Alaska show a high degree of temporal coherence (r = 0.93 – 0.99), which warrants the general conclusion that tundra ponds on Alaska’s Arctic Coastal Plain have undergone a significant change in thermal dynamics over the past four decades. Our results provide a means to incorporate these pond types into larger-scale simulations of Arctic climate change.
Hypertension drives parenchymal β-amyloid accumulation in the brain parenchyma

There is substantial controversy regarding the causative role of amyloid β (Aβ) deposition in Alzheimer's disease (AD). The cerebrovasculature plays an important role in the elimination of Aβ from the brain and hypertension is a well‐known risk factor for AD. In spontaneously hypertensive stroke‐prone rats (SHRSP), an animal model of chronic arterial hypertension, cerebral small vessel disease (CSVD) leads to age‐dependent parenchymal Aβ accumulation similar to that observed in AD. These data approve the neuropathological link between CSVD and AD, confirm the challenge that parenchymal Aβ deposition is a specific marker for AD and disclose the meaning of SHRSP as valid experimental model to investigate the association between hypertension, CSVD, and Aβ plaques.
Ursodeoxycholic acid action on the transport function of the small intestine in normal and cystic fibrosis mice

Ursodeoxycholic acid possesses choleretic and cytoprotective properties and in cystic fibrosis (CF) it is used to treat the hepatobiliary symptoms of the disease. This study investigated the effects of this bile acid on the transport function of the small intestine in normal and CF mice. The effects of ursodeoxycholic acid were monitored as changes in short‐circuit current (SCC) in stripped sheets of small intestine from normal (Swiss MF1) and transgenic CF (Cftrtm2Cam) mice. In ileal sheets from Swiss MF1 mice, mucosal ursodeoxycholic acid caused a biphasic increase in SCC. The first phase was reduced by lowering the mucosal Na+ concentration, while the second phase was inhibited by Cl−‐free conditions, serosal furosemide or mucosal diphenylamine‐2‐carboxylic acid (DPC), suggesting an initial Na+‐dependent bile acid absorption followed by a stimulation of electrogenic Cl− secretion. Serosal application of ursodeoxycholic acid to the ileum and mucosal or serosal application to the mid‐intestine and jejunum elicited a secretory response only. Secretion was Ca2+‐dependent, but did not involve neural mechanisms. Mucosal mast cells, histamine and serotonin (5‐HT) were implicated in the secretory response. Responses in tissues from transgenic wild‐type mice were similar to those obtained with Swiss MF1 mice, but the secretory response to mucosal or serosal application of the bile acid was impaired in CF tissues. In ilea from CF mice the initial absorptive phase of the response to mucosal ursodeoxycholic acid was still observed. It is concluded that ursodeoxycholic acid induces secretion throughout the murine small intestine by a mechanism that involves degranulation of mucosal mast cells. In the ileum Na+‐dependent absorption can also be detected. The secretory response is defective in CF intestine, but the absorptive effect is still present.
Non-Linear Text Regression with a Deep Convolutional Neural Network

Text regression has traditionally been tackled using linear models. Here we present a non-linear method based on a deep convolutional neural network. We show that despite having millions of parameters, this model can be trained on only a thousand documents, resulting in a 40% relative improvement over sparse linear models, the previous state of the art. Further, this method is flexible allowing for easy incorporation of side information such as document meta-data. Finally we present a novel technique for interpreting the effect of different text inputs on this complex non-linear model.
Overexpression of AtLOV1 in Switchgrass Alters Plant Architecture, Lignin Content, and Flowering Time

Background Switchgrass (Panicum virgatum L.) is a prime candidate crop for biofuel feedstock production in the United States. As it is a self-incompatible polyploid perennial species, breeding elite and stable switchgrass cultivars with traditional breeding methods is very challenging. Translational genomics may contribute significantly to the genetic improvement of switchgrass, especially for the incorporation of elite traits that are absent in natural switchgrass populations. Methodology/Principal Findings In this study, we constitutively expressed an Arabidopsis NAC transcriptional factor gene, LONG VEGETATIVE PHASE ONE (AtLOV1), in switchgrass. Overexpression of AtLOV1 in switchgrass caused the plants to have a smaller leaf angle by changing the morphology and organization of epidermal cells in the leaf collar region. Also, overexpression of AtLOV1 altered the lignin content and the monolignol composition of cell walls, and caused delayed flowering time. Global gene-expression analysis of the transgenic plants revealed an array of responding genes with predicted functions in plant development, cell wall biosynthesis, and flowering. Conclusions/Significance To our knowledge, this is the first report of a single ectopically expressed transcription factor altering the leaf angle, cell wall composition, and flowering time of switchgrass, therefore demonstrating the potential advantage of translational genomics for the genetic improvement of this crop.
Loss of Cardiolipin Leads to Perturbation of Acetyl-CoA Synthesis*

Cardiolipin (CL), the signature phospholipid of mitochondrial membranes, plays an important role in mitochondrial processes and bioenergetics. CL is synthesized de novo and undergoes remodeling in the mitochondrial membranes. Perturbation of CL remodeling leads to the rare X-linked genetic disorder Barth syndrome, which shows disparities in clinical presentation. To uncover biochemical modifiers that exacerbate CL deficiency, we carried out a synthetic genetic array screen to identify synthetic lethal interactions with the yeast CL synthase mutant crd1Δ. The results indicated that crd1Δ is synthetically lethal with mutants in pyruvate dehydrogenase (PDH), which catalyzes the conversion of pyruvate to acetyl-CoA. Acetyl-CoA levels were decreased in the mutant. The synthesis of acetyl-CoA depends primarily on the PDH-catalyzed conversion of pyruvate in the mitochondria and on the PDH bypass in the cytosol, which synthesizes acetyl-CoA from acetate. Consistent with perturbation of the PDH bypass, crd1Δ cells grown on acetate as the sole carbon source exhibited decreased growth, decreased acetyl-CoA, and increased intracellular acetate levels resulting from decreased acetyl-CoA synthetase activity. PDH mRNA and protein levels were up-regulated in crd1Δ cells, but PDH enzyme activity was not increased, indicating that PDH up-regulation did not compensate for defects in the PDH bypass. These findings demonstrate for the first time that CL is required for acetyl-CoA synthesis, which is decreased in CL-deficient cells as a result of a defective PDH bypass pathway.
Elevated interferon regulatory factor 4 levels in patients with allergic asthma.

OBJECTIVE Allergic asthma is a common inflammatory disease regulated by the T helper (Th) cells. Interferon regulatory factor 4 (IRF4) plays an important role in the differentiation of Th cells. This study investigated whether IRF4 is involved in the systemic immune responses in allergic asthma patients. METHODS Peripheral blood mononuclear cells (PBMCs) were isolated from allergic asthmatics (n = 29) and healthy controls (n = 12). The mRNA and protein levels of IRF4 in PBMCs were measured by quantitative RT-PCR and western blotting. The frequencies of Th1, Th2, and Th17 cells were analyzed by flow cytometry. The related cytokine (interferon-γ, interleukin-4 (IL-4), and IL-17) concentrations in plasma and culture supernatants were measured by ELISA. The levels of GATA binding protein 3 (GATA3), retinoic acid-related orphan receptor γt (RORγt), and forkhead box P3 (FOXP3), the master transcription factors controlling Th2, Th17, and T regulatory cells differentiation, respectively, were examined by quantitative RT-PCR. RESULTS The levels of IRF4 were elevated in allergic asthmatics compared with those in healthy controls. The frequencies of Th2 and Th17 cells as well as the concentrations of Th2- and Th17-related cytokines were higher in plasma from asthma patients than those from healthy controls; similar results were observed in culture supernatants. IRF4 mRNA levels were positively correlated with GATA3, RORγt, and FOXP3 mRNA levels in allergic asthmatics but not in healthy controls. CONCLUSIONS Our results suggested that IRF4 may play a role in the systemic inflammation of allergic asthma patients by facilitating the differentiation of Th2 and Th17 cells at least at the transcriptional level.
Gene discovery in the wood-forming tissues of poplar: analysis of 5, 692 expressed sequence tags.

A rapidly growing area of genome research is the generation of expressed sequence tags (ESTs) in which large numbers of randomly selected cDNA clones are partially sequenced. The collection of ESTs reflects the level and complexity of gene expression in the sampled tissue. To date, the majority of plant ESTs are from nonwoody plants such as Arabidopsis, Brassica, maize, and rice. Here, we present a large-scale production of ESTs from the wood-forming tissues of two poplars, Populus tremula L. x tremuloides Michx. and Populus trichocarpa 'Trichobel. ' The 5,692 ESTs analyzed represented a total of 3,719 unique transcripts for the two cDNA libraries. Putative functions could be assigned to 2,245 of these transcripts that corresponded to 820 protein functions. Of specific interest to forest biotechnology are the 4% of ESTs involved in various processes of cell wall formation, such as lignin and cellulose synthesis, 5% similar to developmental regulators and members of known signal transduction pathways, and 2% involved in hormone biosynthesis. An additional 12% of the ESTs showed no significant similarity to any other DNA or protein sequences in existing databases. The absence of these sequences from public databases may indicate a specific role for these proteins in wood formation. The cDNA libraries and the accompanying database are valuable resources for forest research directed toward understanding the genetic control of wood formation and future endeavors to modify wood and fiber properties for industrial use.
Blind modulation recognition of PSK signals based on constellation reconstruction

A system based on constellation reconstruction for blind Modulation recognition of MPSK/MDPSK signals in non-cooperative communication applications is proposed. The system requires no prior information about the signal, and parameters needed in the procedure of constellation reconstruction such as carrier frequency, symbol rate and timing information, are estimated from received data samples. And the method of phase difference is used to eliminate the constellation diagram pervasion aroused by carrier frequency offset. Subordinate function is also been proposed and defined in this paper, the function which calculates its value by utilizing clustering number obtained from clustering of the constellation, so different MPSK/MDPSK signals can be classified by different values of the function. In AWGN channel, simulation proved that when SNR>lldB, the recognition ratio are above 90% for all kinds of signals, and for BPSK, 4PSK signals the ratio can achieve 100% when SNR>6dB, it shows the system is effective.