Miracle-dz/UniFAR-FTUs huggingface dataset:
Soluble and membrane levels of molecules involved in the interaction between clonal plasma cells and the immunological microenvironment in multiple myeloma and their association with the characteristics of the disease

Clonal plasma cells (PC) from different types of monoclonal gammopathies (MG) display distinct phenotypes consistent with an increased antigen‐presentation and T‐cell costimulation in MG of undetermined significance that deteriorates in malignant conditions. Expression of other cell surface and soluble molecules (e.g. adhesion/proliferation molecules) involved in the interaction between clonal PC and the bone marrow (BM) microenvironment has also been related to malignant PC, although the exact clinical significance of their expression remains largely unknown. Analysis of cell surface levels of several of these molecules in multiple myeloma (MM) patients shows an association between lower expression on BMPC of the HLA‐I and β2‐microglobulin antigen‐presenting molecules, the CD126 and CD130 IL6 receptor (IL6R) chains, and CD38, and adverse prognostic features of the disease. Likewise, patients showing higher soluble levels of antigen‐presenting molecules (HLA‐I and β2‐microglobulin), IL6R and CD95 tended to be associated with more aggressive disease behavior. In contrast, CD40, CD86, CD56, CD19, and CD45 were not associated with patients' outcome. Interestingly, upon considering the ratio between the soluble and PC membrane expression of each molecule, an increased adverse prognostic impact was observed for both HLA‐I and β2‐microglobulin, but not for the other molecules. Multivariate analysis confirmed the independent prognostic value of cell surface expression of CD126 on BMPC together with serum β2‐microglobulin and LDH. In summary, our results show an abnormal distribution of the cellular and soluble compartments of the HLA‐I, IL6R, and to a lower extent, CD95 molecules, in MM, associated with the clinical characteristics and behavior of the disease. © 2008 Wiley‐Liss, Inc.
Visualizing and Understanding Recurrent Networks

Recurrent Neural Networks (RNNs), and specifically a variant with Long Short-Term Memory (LSTM), are enjoying renewed interest as a result of successful applications in a wide range of machine learning problems that involve sequential data. However, while LSTMs provide exceptional results in practice, the source of their performance and their limitations remain rather poorly understood. Using character-level language models as an interpretable testbed, we aim to bridge this gap by providing an analysis of their representations, predictions and error types. In particular, our experiments reveal the existence of interpretable cells that keep track of long-range dependencies such as line lengths, quotes and brackets. Moreover, our comparative analysis with finite horizon n-gram models traces the source of the LSTM improvements to long-range structural dependencies. Finally, we provide analysis of the remaining errors and suggests areas for further study.
Coastal Tourism and Economic Inclusion in Indian Ocean Rim Association States

The inclusiveness of tourism development is coming under close academic and policy scrutiny, including in policy debates within the Indian Ocean region through the Indian Ocean Rim Association (IORA). Coastal and marine tourism is recognised as a vital Blue Economy sector by IORA countries and in the IORA Action Plan 2017–2021. South Africa, which serves as IORA chair from 2017–2019, has been at the forefront of recent debates around economic inclusion and tourism.
Patterns of prefrontal dysfunction in alcoholics with and without Korsakoff’s syndrome, patients with Parkinson’s disease, and patients with rupture and repair of the anterior communicating artery

This study compared patterns of frontal-lobe dysfunction in alcoholics with Korsakoff’s syndrome (KS: n = 9), non-Korsakoff alcoholics (AL: n = 28), patients with Parkinson’s disease (PD: n = 18), and patients with rupture and repair of the anterior communicating artery (ACoA: n = 4) relative to healthy non-neurological control (NC) participants (n = 70). The tests administered were sensitive to functions of dorsolateral prefrontal and orbito-frontal subsystems. Measures included perseverative errors on the Wisconsin Card Sorting Test (WCST-pe), errors on object alternation (OA), errors on Trails B, number of words generated on the Controlled Oral Word Association Test (COWAT), and number of categories completed on the WCST (WCST-cc). KS patients were as impaired as AL participants on orbitofrontal measures and, on dorsolateral prefrontal measures, were impaired relative to AL participants, whose performance did not differ from controls. Patients with PD also were impaired on tests of orbitofrontal and dorsolateral prefrontal functioning but to a lesser extent than the KS patients. Moreover, most of the PD deficits were driven by the impaired performance of patients whose initial symptoms were on the right side of the body. The ACoA patients were significantly impaired on tests of orbitofrontal but not dorsolateral prefrontal functioning relative to the control group. Together, the results confirm different patterns of frontal-system impairments in patient groups having compromised frontal lobe functioning consequent to varying etiologies.
Phospholemman Phosphorylation Mediates the Protein Kinase C–Dependent Effects on Na+/K+ Pump Function in Cardiac Myocytes

Because phospholemman (PLM) regulates the Na+/K+ pump (NKA) and is a major cardiac phosphorylation target for both protein kinase A (at Ser68) and protein kinase C (PKC) (at both Ser63 and Ser68), we evaluated whether PLM mediates the PKC-dependent regulation of NKA function and protein kinase A/PKC crosstalk in ventricular myocytes. PKC was activated by PDBu (300 nmol/L), and we measured NKA-mediated [Na+]i decline (fluorescence measurements) and current (Ipump) (voltage clamp). In wild-type mouse myocytes, PDBu increased PLM phosphorylation at Ser63 and Ser68, Ipump (both at 10 and 100 mmol/L Na+ in the pipette solution) and maximal NKA-mediated Na+ extrusion rate (Vmax) from 7.9±1.1 to 12.7±1.9 mmol·L−1 per minute without altering NKA affinity for internal Na+ (K0.5). In PLM knockout mice, PDBu had no effect on either Vmax or K0.5. After pretreatment with isoproterenol (ISO) (1 &mgr;mol/L), PDBu still increased the NKA Vmax and PLM phosphorylation at Ser63 and Ser68. Conversely, after pretreatment with PDBu, ISO further increased the Na+ affinity of NKA and phosphorylation at Ser68, as it did alone without PDBu. The final NKA activity was independent of the application sequence. The NKA activity in PLM knockout myocytes, after normalizing the protein level, was similar to that after PDBu and ISO treatment. We conclude that (1) PLM mediates the PKC-dependent activation of NKA function in cardiac myocytes, (2) PDBu and ISO effects are additive in the mouse (affecting mainly Vmax and K0.5, respectively), and (3) PDBu and ISO combine to activate NKA in wild-type to the level found in the PLM knockout mouse.
Conversion of Prevalence Survey Data on Nosocomial Infections to Incidence Estimates: A Simplified Tool for Surveillance?

We calculated the incidence of nosocomial infection in 2 intensive care units (ICUs) on the basis of prevalence data recorded from 1997 through 2002 and compared these estimates to cumulative incidences measured in the 2 ICUs during the same period to investigate the feasibility and the reliability of converting prevalence data to incidence estimates. Decreases in the calculated and measured incidences over time in the ICUs were found to be statistically significantly related.
Cytochrome cbb3 of Thioalkalivibrio is a Na+-pumping cytochrome oxidase

Significance The majority of aerobic living organisms use oxygen for respiration. The key enzyme, which directly reduces oxygen to water during respiration, is the terminal cytochrome c oxidase. It generates a large portion of the utilizable energy provided by the respiratory chain. Accumulation of biologically available energy by means of cytochrome c oxidases is believed to be due to the proton-motive force across the mitochondrial or bacterial membrane. Details of this energy conversion are still unclear. Here we report the discovery of a sodium-pumping cytochrome c oxidase that converts energy of respiration into sodium-motive force. This finding provides clues to understanding the mechanism of cytochrome c oxidase that is not available when applying knowledge of the proton-pumping versions of the enzyme. Cytochrome c oxidases (Coxs) are the basic energy transducers in the respiratory chain of the majority of aerobic organisms. Coxs studied to date are redox-driven proton-pumping enzymes belonging to one of three subfamilies: A-, B-, and C-type oxidases. The C-type oxidases (cbb3 cytochromes), which are widespread among pathogenic bacteria, are the least understood. In particular, the proton-pumping machinery of these Coxs has not yet been elucidated despite the availability of X-ray structure information. Here, we report the discovery of the first (to our knowledge) sodium-pumping Cox (Scox), a cbb3 cytochrome from the extremely alkaliphilic bacterium Thioalkalivibrio versutus. This finding offers clues to the previously unknown structure of the ion-pumping channel in the C-type Coxs and provides insight into the functional properties of this enzyme.
EFFECTS OF TIME AFTER INFECTION, MOSQUITO GENOTYPE, AND INFECTIOUS VIRAL DOSE ON THE DYNAMICS OF CULEX TARSALIS VECTOR COMPETENCE FOR WESTERN EQUINE ENCEPHALOMYELITIS VIRUS

ABSTRACT The vector competence of Culex tarsalis Coquillett for the BFS1703 strain of western equine encephalomyelitis virus (WEEV) changed significantly as a function of time after infection, mosquito genotype, and infectious virus dose. After ingesting a high virus dose (5 log10 plaque-forming units [PFU]/0.1 ml), females of the susceptible high virus producer (HVP) strain rapidly amplified virus, developed a disseminated infection, and efficiently transmitted WEEV by 4 days postinfection (dpi). The quantity of virus expectorated peaked at 4 dpi (mean 3.4 log10 PFU), and the percentage of females transmitting per os peaked at 7 dpi (80%); both measures of transmission subsequently decreased to low levels throughout the remainder of infected life. HVP females imbibing a low virus dose (3 log10 PFU/0.1 ml) were infected less frequently and took longer to amplify virus to levels recorded for the high virus dose group and did not transmit virus efficiently, thereby indicating midgut infection and escape barriers were dose and time dependent. These data emphasized the importance of elevated avian viremias in Cx. tarsalis vector competence. Females from the WEEV-resistant (WR) strain and two wild-type strains from Kern and Riverside counties were significantly less susceptible to infection at both high and low doses than was the HVP strain. Overall, females with a high virus titer more frequently had a disseminated infection, but there did not seem to be a distinct threshold demarcating this relationship. In marked contrast, all infected females transmitting virus had body titers >4.3 log10 PFU, and most had titers >4.8 log10 PFU. These data indicated that not all females with a disseminated infection transmitted virus because of the presence of one or more salivary gland barriers.
Near-Infrared Classification Spectroscopy: J-Band Spectra of Fundamental MK Standards

We present a catalog of J-band spectra for 88 fundamental MK standard stars observed at a resolving power of R ~ 3000. This contribution serves as a companion atlas to the K-band spectra recently published by Wallace & Hinkle and the H-band atlas by Meyer and coworkers. We report data from 7400 to 9550 cm-1 (1.05-1.34 μm) for stars of spectral types O7-M6 and luminosity classes I-V as defined in the MK system. In reducing these data, special care has been taken to remove time-variable telluric features of water vapor. We identify atomic and molecular indexes that are both temperature and luminosity sensitive that aid in the classification of stellar spectra in the J band. In addition to being useful in the classification of late-type stars, the J band contains several features of interest in the study of early-type stellar photospheres. These data are available electronically for anonymous FTP in addition to being served on the World Wide Web.
Carbon Sequestration and Fertility after Centennial Time Scale Incorporation of Charcoal into Soil

The addition of pyrogenic carbon (C) in the soil is considered a potential strategy to achieve direct C sequestration and potential reduction of non-CO2 greenhouse gas emissions. In this paper, we investigated the long term effects of charcoal addition on C sequestration and soil physico-chemical properties by studying a series of abandoned charcoal hearths in the Eastern Alps of Italy established in the XIX century. This natural setting can be seen as an analogue of a deliberate experiment with replications. Carbon sequestration was assessed indirectly by comparing the amount of pyrogenic C present in the hearths (23.3±4.7 kg C m−2) with the estimated amount of charcoal that was left on the soil after the carbonization (29.3±5.1 kg C m−2). After taking into account uncertainty associated with parameters’ estimation, we were able to conclude that 80±21% of the C originally added to the soil via charcoal can still be found there and that charcoal has an overall Mean Residence Time of 650±139 years, thus supporting the view that charcoal incorporation is an effective way to sequester atmospheric CO2. We also observed an overall change in the physical properties (hydrophobicity and bulk density) of charcoal hearth soils and an accumulation of nutrients compared to the adjacent soil without charcoal. We caution, however, that our site-specific results should not be generalized without further study.
Cauda Equina Syndrome Caused by Spinal Dural Arteriovenous Fistula

Spinal dural arteriovenous fistula (SDAVF) is rare but still the most commonly encountered vascular malformation of the spinal cord. A 31-year-old male developed gait disturbance due to weakness of his lower extremities, voiding difficulty and sexual dysfunction with a progressive course since 3 months. He showed areflexia in both knees and ankles. Electromyographic findings were suggestive of multiple root lesions involving bilateral L2 to S4 roots of moderate degree. Magnetic resonance images showed high signal intensity with an ill-defined margin in T2-weighted images and intensely enhanced by a contrast agent through the lumbosacral spinal cord. Selective spinal angiography confirmed a dural arteriovenous fistula with a nidus at the L2 vertebral level. After selective endovascular embolization, his symptoms drastically improved except sexual dysfunction. We report a rare case of cauda equina syndrome due to spinal arteriovenous fistula with drastic improvement after endovascular embolization.
Detection of polymerase chain reaction-amplified human immunodeficiency virus type 1 proviral DNA with a digoxigenin-labeled RNA probe and an enzyme-linked immunoassay

An enzyme-linked immunoassay (EIA) combined with a solution hybridization (SH) reaction was devised to detect human immunodeficiency virus type 1 (HIV-1) provirus amplified by the polymerase chain reaction (PCR). In this nonisotopic PCR assay, designated PCR-EIASH, a fragment of the HIV-1 gag gene from peripheral blood mononuclear cells (PBMCs) was first amplified with biotinylated primers. The biotinylated amplified DNA segment was reacted in solution with an internal RNA probe labeled with digoxigenin-11-UTP. Hybrids were captured in a microtiter plate coated with streptavidin. Specific bound hybrids were quantitated by the addition of an enzyme-labeled antibody against digoxigenin and a fluorogenic substrate. The hybridization, immunological, and amplification parameters of PCR-EIASH were optimized as follows: 12.5 pmol of each primer was used in the PCR; the reannealing reaction of amplified products with the RNA probe, which was used at 0.30 microgram/ml, was completed in 30 min at 70 degrees C in 2x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate). Five copies of HIV-1 DNA diluted in a lysate of 100,000 PBMCs from a seronegative control could be detected by PCR-EIASH with a signal of 41 +/- 3 fluorescent units above a background noise of 13 +/- 2 fluorescent units. A total of 91 PBMC lysates from 91 seropositive patients sampled once and 20 PBMC lysates from 10 seropositive patients sampled twice were tested in duplicate in the PCR-EIASH; 107 samples were positive in duplicate tests, 1 sample was indeterminate, and 3 samples were negative. Of the latter three samples, one became positive by diluting the cell lysate, suggesting the presence of an inhibitor of Taq polymerase. The three samples negative for HIV-1 by PCR-EIASH were also negative when amplified with SK145-SK39 and detected with 32P-labeled SK102.
How Bad is the Problem of PP-Attachment? A Comparison of English, German and Swedish

The correct attachment of prepositional phrases (PPs) is a central disambiguation problem in parsing natural languages. This paper compares the baseline situation in English, German and Swedish based on manual PP attachments in various tree-banks for these languages. We argue that cross-language comparisons of the disam-biguation results in previous research is impossible because of the different selection procedures when building the training and test sets. We perform uniform tree-bank queries and show that English has the highest noun attachment rate followed by Swedish and German. We also show that the high rate in English is dominated by the preposition of . From our study we derive a list of criteria for proﬁling data sets for PP attachment experiments.
Atomic structure reveals the unique capsid organization of a dsRNA virus

For most dsRNA viruses, the genome-enclosing capsid comprises 120 copies of a single capsid protein (CP) organized into 60 icosahedrally equivalent dimers, generally identified as 2 nonsymmetricallyinteracting CP molecules with extensive lateral contacts. The crystal structure of a partitivirus, Penicillium stoloniferum virus F (PsV-F), reveals a different organization, in which the CP dimer is related by almost-perfect local 2-fold symmetry, forms prominent surface arches, and includes extensive structure swapping between the 2 subunits. An electron cryomicroscopy map of PsV-F shows that the disordered N terminus of each CP molecule interacts with the dsRNA genome and probably participates in its packaging or transcription. Intact PsV-F particles mediate semiconservative transcription, and transcripts are likely to exit through negatively charged channels at the icosahedral 5-fold axes. Other findings suggest that the PsV-F capsid is assembled from dimers of CP dimers, with an arrangement similar to flavivirus E glycoproteins.
Time-resolved chirp of Pre-Impulse Step Injected Current modulated Semiconductor Optical Amplifier

Using Pre-Impulse Step Injected Current (PISIC) technique, it is possible to significantly improve the Semiconductor Optical Amplifier (SOA) rising time, although that will also affect chirp. Therefore, it is important to make a quantifying analysis of the event. The measurements are made using the intensity to frequency conversion provided by sharp optical filters. In this work two fixed filters are used instead of one alone, as available in the literature. The results evince chirp peaks during the SOA off-on gain rising time and at the on-off gain decay. The chirp values we found are coherent with published results.
Reactive oxygen species regulate prosurvival ERK1/2 signaling and bFGF expression in gliosis within the retina.

PURPOSE Gliosis is the response of glial cells within retinal tissue to injury. It can be beneficial in the short term, but if the response is extended it can lead to scar formation, which contributes to blindness. Phosphorylation of extracellular signal regulated kinase 1/2 (ERK1/2) is considered to be a hallmark event of gliosis, but the factors involved throughout its associated signaling pathway remain poorly understood, particularly in the retina. Because reactive oxygen species (ROS) can inhibit phosphatases, thereby altering the phosphorylation of proteins, this study tested the hypothesis that ROS regulate the phosphorylation of ERK1/2 (pERK1/2) in gliosis. METHODS Increases in pERK1/2 were detected using Western blotting and immunofluorescence in three models of retinal stress, specifically the in vivo light induction, the rd1 disease, and the ex vivo retinal explant models. Explanted murine retinas were used to identify the signaling partners of pERK1/2 via Western blotting, in conjunction with inhibitors. The effect of this pathway on cell death was measured with terminal dUTP nick end labeling. RESULTS It was demonstrated that several inhibitors of ROS greatly reduce the levels of pERK1/2 in the somata of Müller cells and furthermore decrease two other downstream signaling events: the phosphorylation of STAT3 and the upregulation of basic fibroblast growth factor. Using the specific inhibitor of ERK1/2, UO126, the resultant outcomes of this signaling pathway were determined to contribute significantly to cell survival. CONCLUSIONS The novel finding of this study that ROS contribute to a prosurvival signaling pathway in retinal Müller cell gliosis indicates that some degree of caution should be used when considering antioxidants as therapeutics.
Polycystic Ovarian Syndrome Association study of calpain-10 Gene Polymorphism in Patients with Polycystic Ovarian Syndrome

Polycystic Ovarian syndrome (PCOS) is a common endocrine disorder with a global prevalence of 5-10% among women of reproductive age. PCOS is characterized by chronic anovulation, polycystic ovaries, hyperandrogenism, hirsutism, overweight, insulin resistance, and infertility. It is well-known that PCOS is a complex trait similar to type-2 diabetes in which both genetic and environmental factors play a crucial role in the pathogenesis of the disease. A couple of type-2 diabetes susceptibility genes including those for insulin secretion and action such as Calpain-10 have shown considerable contribution to genetic predisposition to PCOS. Since Calpain-10 gene seems to be a strong candidate gene for PCOS, we aimed to investigate the role of Caplain-10 gene polymorphism UCSNP-44 (T/C) located in a transcription enhancer element of the gene in disease susceptibility. We carried out a cross-sectional case-control study. Using simple random sampling, ninety healthy women were selected. All ninety patients fulfilled the 2003 Rotterdam criteria of PCOS. The subjects were genotyped for Caplain-10 gene polymorphism UCSNP-44 (T/C) using PCR-RFLP. Differences in genotype distributions between case and control subjects were examined via the chi-square test. Although PCOS showed a high prevalence among women in Bandar Abbas, Caplain-10 gene polymorphism UCSNP-44 (T/C) UCSNP44 did not influence the susceptibility to PCOS.