Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental verification of a new model describing the influence of incomplete signal extinction ratio on the sensitivity degradation due to multiple interferometric crosstalk

Larger optical penalties than predicted by a Gaussian crosstalk model are found both in our experiments and in the literature when investigating signals including multiple interferometric crosstalk contributions. We attribute this to an imperfect signal extinction ratio. In this letter, simple analytical relations for crosstalk induced power penalties are derived taking the signal extinction ratio into account and excellent agreement with 10-Gb/s experiments is obtained. Both theory and experiments show the importance of the signal extinction ratio in connection with interferometric crosstalk.
Combining NLP and probabilistic categorisation for document and term selection for Swiss-Prot medical annotation

MOTIVATION Searching relevant publications for manual database annotation is a tedious task. In this paper, we apply a combination of Natural Language Processing (NLP) and probabilistic classification to re-rank documents returned by PubMed according to their relevance to Swiss-Prot annotation, and to identify significant terms in the documents. RESULTS With a Probabilistic Latent Categoriser (PLC) we obtained 69% recall and 59% precision for relevant documents in a representative query. As the PLC technique provides the relative contribution of each term to the final document score, we used the Kullback-Leibler symmetric divergence to determine the most discriminating words for Swiss-Prot medical annotation. This information should allow curators to understand classification results better. It also has great value for fine-tuning the linguistic pre-processing of documents, which in turn can improve the overall classifier performance.
Proceedings of the Credibility Assessment and Information Quality in Government and Business Symposium

This paper presents findings from an eye tracker experiment based on the guilty knowledge test (GKT) paradigm. We conducted a two-group, posttest-only, randomized initial experiment in which the guilty group constructed an improvised explosive device (IED) and then was screened by an embodied conversational agent (ECA). Participants in the control condition went straight to screening. During the screening interview, participants were shown three images. The second image was a modified picture of an IED similar to the one constructed by the guilty participants. Eye gaze behavior was dramatically different between the groups. A classification algorithm correctly classified 100% of the participants as either part of the guilty or control group.
Conservation of Complex Nuclear Localization Signals Utilizing Classical and Non-Classical Nuclear Import Pathways in LANA Homologs of KSHV and RFHV

ORF73 latency-associated nuclear antigen (LANA) of the Kaposi's sarcoma-associated herpesvirus (KSHV) is targeted to the nucleus of infected cells where it binds to chromatin and mediates viral episome persistence, interacts with cellular proteins and plays a role in latency and tumorigenesis. A structurally related LANA homolog has been identified in the retroperitoneal fibromatosis herpesvirus (RFHV), the macaque homolog of KSHV. Here, we report the evolutionary and functional conservation of a novel bi-functional nuclear localization signal (NLS) in KSHV and RFHV LANA. N-terminal peptides from both proteins were fused to EGFP or double EGFP fusions to examine their ability to induce nuclear transport of a heterologous protein. In addition, GST-pull down experiments were used to analyze the ability of LANA peptides to interact with members of the karyopherin family of nuclear transport receptors. Our studies revealed that both LANA proteins contain an N-terminal arginine/glycine (RG)-rich domain spanning a conserved chromatin-binding motif, which binds directly to importin β1 in a RanGTP-sensitive manner and serves as an NLS in the importin β1-mediated non-classical nuclear import pathway. Embedded within this domain is a conserved lysine/arginine-(KR)-rich bipartite motif that binds directly to multiple members of the importin α family of nuclear import adaptors in a RanGTP-insensitive manner and serves as an NLS in the classical importin α/β-mediated nuclear import pathway. The positioning of a classical bipartite kr-NLS embedded within a non-classical rg-NLS is a unique arrangement in these viral proteins, whose nuclear localization is critical to their functionality and to the virus life cycle. The ability to interact with multiple import receptors provides alternate pathways for nuclear localization of LANA. Since different import receptors can import cargo to distinct subnuclear compartments, a multifunctional NLS may provide LANA with an increased ability to interact with different nuclear components in its multifunctional role to maintain viral latency.
Desulfovibrio desulfuricans PglB homolog possesses oligosaccharyltransferase activity with relaxed glycan specificity and distinct protein acceptor sequence requirements.

Oligosaccharyltransferases (OTases) are responsible for the transfer of carbohydrates from lipid carriers to acceptor proteins and are present in all domains of life. In bacteria, the most studied member of this family is PglB from Campylobacter jejuni (PglB(Cj)). This enzyme is functional in Escherichia coli and, contrary to its eukaryotic counterparts, has the ability to transfer a variety of oligo- and polysaccharides to protein carriers in vivo. Phylogenetic analysis revealed that in the delta proteobacteria Desulfovibrio sp. , the PglB homolog is more closely related to eukaryotic and archaeal OTases than to its Campylobacter counterparts. Genetic analysis revealed the presence of a putative operon that might encode all enzymes required for N-glycosylation in Desulfovibrio desulfuricans. D. desulfuricans PglB (PglB(Dd)) was cloned and successfully expressed in E. coli, and its activity was confirmed by transferring the C. jejuni heptasaccharide onto the model protein acceptor AcrA. In contrast to PglB(Cj), which adds two glycan chains to AcrA, a single oligosaccharide was attached to the protein by PglB(Dd). Site-directed mutagenesis of the five putative N-X-S/T glycosylation sites in AcrA and mass spectrometry analysis showed that PglB(Dd) does not recognize the "conventional bacterial glycosylation sequon" consisting of the sequence D/E-X(1)-N-X(2)-S/T (where X(1) and X(2) are any amino acid except proline), and instead used a different site for the attachment of the oligosaccharide than PglB(Cj.). Furthermore, PglB(Dd) exhibited relaxed glycan specificity, being able to transfer mono- and polysaccharides to AcrA. Our analysis constitutes the first characterization of an OTase from delta-proteobacteria involved in N-linked protein glycosylation.
Instruction level power model and its application to general purpose processors

Increased use of portable applications has placed severe limitations on the power consumed by processors and systems. This is particularly true for digital signal processors. Many researchers are now considering power minimization through modification of the high level software and the algorithms. This however will be more effective if a realistic power model for the instructions and the various types of memory accesses were developed. The power consumed in the fetch and the execution of any instruction is dependent on a number of factors, including the state of various functional units associated with the operation and their input patterns. This requires a careful model for the power consumption for any instruction. This paper presents a metric for such a model and its use in determining the power consumption for a given program. This is then used to rewrite the code to achieve considerable power reduction.
Extracellular metabolism of pulmonary surfactant: the role of a new serine protease.

Lung surfactant, an organized complex of lipids and specific apoproteins that is responsible for maintaining alveolar stability, is a product of alveolar epi­ thelial type II cells in which it is packaged for secretion in the form of lamellar bodies (LB) (41, 43, 44). Following its release from type II cells into the alveolar fluid-lining layer, surfactant undergoes a number of structural and metabolic changes. Ultimately, some of the extracellular surfactant is taken back into type II cells for recycling, and the remainder is probably removed by alveolar clearance mechanisms. The structural transformation that surfac­ tant undergoes after its secretion from the type II cell includes at least one step requiring the action of a recently discovered enzyme. We review the evidence for enzymatic activity in this sequence, what is known of its role and actions, as well as some of the properties of the putative enzyme, which we call surfactant convertase.
Mismatch-repair protein MSH6 is associated with Ku70 and regulates DNA double-strand break repair

MSH6, a key component of the MSH2–MSH6 complex, plays a fundamental role in the repair of mismatched DNA bases. Herein, we report that MSH6 is a novel Ku70-interacting protein identified by yeast two-hybrid screening. Ku70 and Ku86 are two key regulatory subunits of the DNA-dependent protein kinase, which plays an essential role in repair of DNA double-strand breaks (DSBs) through the non-homologous end-joining (NEHJ) pathway. We found that association of Ku70 with MSH6 is enhanced in response to treatment with the radiomimetic drug neocarzinostatin (NCS) or ionizing radiation (IR), a potent inducer of DSBs. Furthermore, MSH6 exhibited diffuse nuclear staining in the majority of untreated cells and forms discrete nuclear foci after NCS or IR treatment. MSH6 colocalizes with γ-H2AX at sites of DNA damage after NCS or IR treatment. Cells depleted of MSH6 accumulate high levels of persistent DSBs, as detected by formation of γ-H2AX foci and by the comet assay. Moreover, MSH6-deficient cells were also shown to exhibit impaired NHEJ, which could be rescued by MSH6 overexpression. MSH6-deficient cells were hypersensitive to NCS- or IR-induced cell death, as revealed by a clonogenic cell-survival assay. These results suggest a potential role for MSH6 in DSB repair through upregulation of NHEJ by association with Ku70.
Visfatin Impairs Endothelium-Dependent Relaxation in Rat and Human Mesenteric Microvessels through Nicotinamide Phosphoribosyltransferase Activity

Visfatin, also known as extracellular pre–B-cell colony–enhancing factor (PBEF) and nicotinamide phosphoribosyltransferase (Nampt), is an adipocytokine whose circulating levels are enhanced in metabolic disorders, such as type 2 diabetes mellitus and obesity. Circulating visfatin levels have been positively associated with vascular damage and endothelial dysfunction. Here, we investigated the ability of visfatin to directly impair vascular reactivity in mesenteric microvessels from both male Sprague-Dawley rats and patients undergoing non-urgent, non-septic abdominal surgery. The pre-incubation of rat microvessels with visfatin (50 and 100 ng/mL) did not modify the contractile response to noradrenaline (1 pmol/L to 30 µmol/L), as determined using a small vessel myograph. However, visfatin (10 to 100 ng/mL) concentration-dependently impaired the relaxation to acetylcholine (ACh; 100 pmol/L to 3 µmol/L), without interfering with the endothelium-independent relaxation to sodium nitroprusside (1 nmol/L to 3 µmol/L). In both cultured human umbilical vein endothelial cells and rat microvascular preparations, visfatin (50 ng/mL) stimulated nicotinamide adenine dinucleotide phosphate (NADPH) oxidase activity, as determined by lucigenin-derived chemiluminiscence. The relaxation to ACh impaired by visfatin was restored by the NADPH oxidase inhibitor apocynin (10 µmol/L). Additionally, the Nampt inhibitor APO866 (10 mmol/L to 10 µmol/L), but not an insulin receptor-blocking antibody, also prevented the stimulation of NADPH oxidase and the relaxation impairment elicited by visfatin. Accordingly, the product of Nampt activity nicotinamide mononucleotide (100 nmol/L to 1 mmol/L) stimulated endothelial NADPH oxidase activity and concentration-dependently impaired ACh-induced vasorelaxation. In human mesenteric microvessels pre-contracted with 35 mmol/L potassium chloride, the endothelium-dependent vasodilation to bradykinin (1 nmol/L to 3 µmol/L) was equally impaired by visfatin and restored upon co-incubation with APO866. In conclusion, visfatin impairs endothelium-dependent relaxation through a mechanism involving NADPH oxidase stimulation and relying on Nampt enzymatic activity, and therefore arises as a potential new player in the development of endothelial dysfunction.
Expression of Cu/Zn and Mn superoxide dismutases during bovine embryo development: Influence of in vitro culture

Temporal pattern of expression of Cu/Zn and Mn superoxide dismutases (SODs) was investigated in bovine oocytes and embryos produced in vitro in two different culture conditions and in vivo after superovulation. SODs were examined at a transcriptional level in single oocytes and embryos by reverse transcriptase–polymerase chain reaction (RT‐PCR) and, at a protein level, by Western blotting on pools of embryos. mRNA encoding Cu/Zn SOD were detected in in vitro bovine embryos throughout preattachment development as well as in in vivo derived morulae and blastocysts. Transcripts for Mn SOD gene were detected in most immature and in vitro matured oocytes as well as in some zygotes and 5‐ to 8‐cell embryos while no transcript was found at the 9‐ to 16‐cell stage in both culture conditions. In vitro embryonic expression of Mn SOD was detected earlier in the presence of serum. Half of the morulae showed the transcript if cultured with 5% serum while none without serum. At the blastocyst stage Mn SOD could be detected independently of culture conditions. For in vivo–derived embryos Mn SOD transcripts were detected both in morulae and blastocysts. Immunoblotting analyses revealed that Cu/Zn SOD and Mn SOD were also present at a protein level in in vitro‐derived zygotes and blastocysts. Together these data demonstrate, for the first time, that Mn SOD is transcribed and that Cu/Zn and Mn SOD proteins are expressed in preimplantation bovine embryos. Finally, they suggest that Mn SOD transcription is altered by in vitro culture conditions. Mol. Reprod. Dev. 58:45–53, 2001. © 2001 Wiley‐Liss, Inc.
Sprint performance is related to muscle fascicle length in male 100-m sprinters.

The purpose of this study was to investigate the relationship between muscle fascicle length and sprint running performance in 37 male 100-m sprinters. The sample was divided into two performance groups by the personal-best 100-m time: 10.00-10.90 s (S10; n = 22) and 11.00-11.70 s (S11; n = 15). Muscle thickness and fascicle pennation angle of the vastus lateralis and gastrocnemius medialis and lateralis muscles were measured by B-mode ultrasonography, and fascicle length was estimated. Standing height, body weight, and leg length were similar between groups. Muscle thickness was similar between groups for vastus lateralis and gastrocnemius medialis, but S10 had a significantly greater gastrocnemius lateralis muscle thickness. S10 also had a greater muscle thickness in the upper portion of the thigh, which, given similar limb lengths, demonstrates an altered "muscle shape. " Pennation angle was always less in S10 than in S11. In all muscles, S10 had significantly greater fascicle length than did S11, which significantly correlated with 100-m best performance (r values from -0.40 to -0.57). It is concluded that longer fascicle length is associated with greater sprinting performance.
In vivo measurement of dose distribution in patients' lymphocytes: helical tomotherapy versus step-and-shoot IMRT in prostate cancer

Abstract In radiotherapy, in vivo measurement of dose distribution within patients' lymphocytes can be performed by detecting gamma-H2AX foci in lymphocyte nuclei. This method can help in determining the whole-body dose. Options for risk estimations for toxicities in normal tissue and for the incidence of secondary malignancy are still under debate. In this investigation, helical tomotherapy (TOMO) is compared with step-and-shoot IMRT (SSIMRT) of the prostate gland by measuring the dose distribution within patients' lymphocytes. In this prospective study, blood was taken from 20 patients before and 10 min after their first irradiation fraction for each technique. The isolated leukocytes were fixed 2 h after radiation. DNA double-stranded breaks in lymphocyte nuclei were stained immunocytochemically using anti-gamma-H2AX antibodies. Gamma-H2AX foci distribution in lymphocytes was determined for each patient. Using a calibration line, dose distributions in patients' lymphocytes were determined by studying the gamma-H2AX foci distribution, and these data were used to generate a cumulative dose–lymphocyte histogram (DLH). Measured in vivo (DLH), significantly fewer lymphocytes indicated low-dose exposure (<40% of the applied dose) during TOMO compared with SSIMRT. The dose exposure range, between 45 and 100%, was equal with both radiation techniques. The mean number of gamma-H2AX foci per lymphocyte was significantly lower in the TOMO group compared with the SSIMRT group. In radiotherapy of the prostate gland, TOMO generates a smaller fraction of patients' lymphocytes with low-dose exposure relative to the whole body compared with SSIMRT. Differences in the constructional buildup of the different linear accelerator systems, e.g. the flattening filter, may be the cause thereof. The influence of these methods on the incidence of secondary malignancy should be investigated in further studies.
Prevention of travelers' diarrhea with rifaximin in US travelers to Mexico.

BACKGROUND Because bacterial pathogens are the primary cause of travelers' diarrhea (TD), antibiotic prophylaxis is effective in TD prevention. This study assessed the efficacy and safety of the nonsystemic antibiotic rifaximin in preventing TD in US travelers to Mexico. METHODS Healthy adult students traveling to Mexico received rifaximin 600 mg/d or placebo for 14 days and were followed for 7 days post-treatment. Stool pattern and gastrointestinal symptoms were recorded in daily diary entries. The primary end point was prevention of TD during 14 days of treatment measured by time to first unformed stool. RESULTS A total of 210 individuals received rifaximin (n = 106) or placebo (n = 104) and were included in the safety population. Median age was 21 years (range, 18-75 y), and the majority of participants were female (65%). Efficacy analyses were conducted in a modified intent-to-treat population of 201 patients who received rifaximin (n = 99) or placebo (n = 102). Rifaximin prophylaxis reduced risk of developing TD versus placebo (p < 0.0001). A smaller percentage of individuals who received rifaximin versus placebo developed all-cause TD (20% vs 48%, respectively; p < 0.0001) or TD requiring antibiotic therapy (14% vs 32%, respectively; p = 0.003). More individuals in the rifaximin group (76%) completed treatment without developing TD versus those in the placebo group (51%; p = 0.0004). Rifaximin provided a 58% protection rate against TD and was associated with fewer adverse events than placebo. CONCLUSIONS Prophylactic treatment with rifaximin 600 mg/d for 14 days safely and effectively reduced the risk of developing TD in US travelers to Mexico. Rifaximin chemoprevention should be considered for TD in appropriate individuals traveling to high-risk regions.
Fiscal Policy in an Expectations Driven Liquidity Trap ∗

We examine the impact of fiscal policy interventions in an environment where the short term nominal interest rate is at the zero bound. In the basic New Keynesian model in which the monetary authority operates a Taylor rule, globally multiple equilibria arise, some of which display all the features of a liquidity trap. A loss in confidence can set the economy on a deflationary path that eventually prevents the monetary authority from adjusting the interest rate and can lead to potentially very large output drops. Contrary to a line of recent papers, we find that demand stimulating policies become less effective in a liquidity trap than in normal circumstances. The key reason is that demand stimulus leads agents to believe that things are even worse than they thought. In contrast, supply side policies, such as cuts in labor income taxes, lead to relative optimism and become more powerful.
Merged-Output Hidden Markov Model for Score Following of MIDI Performance with Ornaments, Desynchronized Voices, Repeats and Skips

A score-following algorithm for polyphonic MIDI performances is presented that can handle performance mistakes, ornaments, desynchronized voices, arbitrary repeats and skips. The algorithm is derived from a stochastic performance model based on hidden Markov model (HMM), and we review the recent development of model construction. In this paper, the model is further extended to capture the multi-voice structure, which is necessary to handle note reorderings by desynchronized voices and widely stretched ornaments in polyphony. For this, we propose mergedoutput HMM, which describes performed notes as merged outputs frommultiple HMMs, each corresponding toa voice part. It is confirmed that the model yields a score-following algorithm which is effective under frequent note reorderings across voices and complicated ornaments.
Development and validation of an English version of the Coronary Artery Disease Education Questionnaire (CADE‐Q)

Background: The Coronary Artery Disease Education Questionnaire (CADE‐Q) is a validated specific tool used to assess the knowledge and educate coronary patients in cardiac rehabilitation on aspects related to coronary artery disease (CAD). The aim of this study is to translate, cross‐culturally adapt and validate from Portuguese to English the Coronary Artery Disease Education Questionnaire (CADE‐Q). Methods: Two independent translations were performed by qualified translators. After back‐translation, both versions were reviewed by a committee of experts. A final English version was tested in a pilot study. For the psychometric validation, the tool was administered to 200 Canadian coronary patients enrolled in cardiac rehabilitation (CR). The internal consistency was assessed using Cronbach's alpha, the test–retest reliability using intraclass correlation coefficient (ICC), and the construct validity through factor analysis. Criterion validity of CADE-Q was assessed with regard to patients’ characteristics. Results: Eleven of 19 questions were modified and culturally adapted in the English version. Cronbach's alpha was 0.809 and ICC was 0.846. Factor analysis revealed five factors, all internally consistent and well defined by the items. Criterion validity was supported by significant differences in mean scores by family income (p = 0.02) and educational level (p < 0.001). Conclusion: The English version of the CADE-Q was demonstrated to have adequate reliability and validity, supporting its use in further studies.
Compositional Matrix-Space Models of Language

We propose CMSMs, a novel type of generic compositional models for syntactic and semantic aspects of natural language, based on matrix multiplication. We argue for the structural and cognitive plausibility of this model and show that it is able to cover and combine various common compositional NLP approaches ranging from statistical word space models to symbolic grammar formalisms.