Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning New Semi-Supervised Deep Auto-encoder Features for Statistical Machine Translation

In this paper, instead of designing new features based on intuition, linguistic knowledge and domain, we learn some new and effective features using the deep autoencoder (DAE) paradigm for phrase-based translation model. Using the unsupervised pre-trained deep belief net (DBN) to initialize DAE’s parameters and using the input original phrase features as a teacher for semi-supervised fine-tuning, we learn new semi-supervised DAE features, which are more effective and stable than the unsupervised DBN features. Moreover, to learn high dimensional feature representation, we introduce a natural horizontal composition of more DAEs for large hidden layers feature learning. On two ChineseEnglish tasks, our semi-supervised DAE features obtain statistically significant improvements of 1.34/2.45 (IWSLT) and 0.82/1.52 (NIST) BLEU points over the unsupervised DBN features and the baseline features, respectively.
Homologous Recombination Mediates Functional Recovery of Dysferlin Deficiency following AAV5 Gene Transfer

The dysferlinopathies comprise a group of untreatable muscle disorders including limb girdle muscular dystrophy type 2B, Miyoshi myopathy, distal anterior compartment syndrome, and rigid spine syndrome. As with other forms of muscular dystrophy, adeno-associated virus (AAV) gene transfer is a particularly auspicious treatment strategy, however the size of the DYSF cDNA (6.5 kb) negates packaging into traditional AAV serotypes known to express well in muscle (i.e. rAAV1, 2, 6, 8, 9). Potential advantages of a full cDNA versus a mini-gene include: maintaining structural-functional protein domains, evading protein misfolding, and avoiding novel epitopes that could be immunogenic. AAV5 has demonstrated unique plasticity with regards to packaging capacity and recombination of virions containing homologous regions of cDNA inserts has been implicated in the generation of full-length transcripts. Herein we show for the first time in vivo that homologous recombination following AAV5.DYSF gene transfer leads to the production of full length transcript and protein. Moreover, gene transfer of full-length dysferlin protein in dysferlin deficient mice resulted in expression levels sufficient to correct functional deficits in the diaphragm and importantly in skeletal muscle membrane repair. Intravascular regional gene transfer through the femoral artery produced high levels of transduction and enabled targeting of specific muscle groups affected by the dysferlinopathies setting the stage for potential translation to clinical trials. We provide proof of principle that AAV5 mediated delivery of dysferlin is a highly promising strategy for treatment of dysferlinopathies and has far-reaching implications for the therapeutic delivery of other large genes.
On the new method for the control of discrete nonlinear dynamic systems using neural networks

This correspondence points out an incorrect statement in Adetona et al, 2000, and Adetona et al., 2004, about the application of the proposed control law to nonminimum phase systems. A counterexample shows the limitations of the control law and, furthermore, its control capability to nonminimum phase systems is explained.
Effects of Preterm Birth on Intrinsic Fluctuations in Neonatal Cerebral Activity Examined Using Optical Imaging

Medical advancements in neonatology have significantly increased the number of high-risk preterm survivors. However, recent long-term follow-up studies have suggested that preterm infants are at risk for behavioral, educational, and emotional problems. Although clear relationships have been demonstrated between preterm infants and developmental problems during childhood and adolescence, less is known about the early indications of these problems. Recently, numerous studies on resting-state functional connectivity (RSFC) have demonstrated temporal correlations of activity between spatially remote cortical regions not only in healthy adults but also in neuropathological disorders and early childhood development. In order to compare RSFC of the cerebral cortex between preterm infants at term-equivalent ages and full-term neonates without any anatomical abnormality risk during natural sleep, we used an optical topography system, which is a recently developed extension of near-infrared spectroscopy. We clarified the presence of RSFC in both preterm infants and full-term neonates and showed differences between these groups. The principal differences were that on comparison of RSFC between the bilateral temporal regions, and bilateral parietal regions, RSFC was enhanced in preterm infants compared with full-term neonates; whereas on comparison of RSFC between the left temporal and left parietal regions, RSFC was enhanced in full-term neonates compared with preterm infants. We also demonstrated a difference between the groups in developmental changes of RSFC related to postmenstrual age. Most importantly, these findings suggested that preterm infants and full-term neonates follow different developmental trajectories during the perinatal period because of differences in perinatal experiences and physiological and structural development.
A Novel Approach for Producing Lentiviruses That Are Limited to a Single Cycle of Infection

ABSTRACT We have devised a novel approach for producing simian immunodeficiency virus (SIV) strains and, potentially, human immunodeficiency virus type 1 (HIV-1) strains that are limited to a single cycle of infection. Unlike previous lentiviral vectors, our single-cycle SIV is capable of expressing eight of the nine viral gene products and infected cells release immature virus particles that are unable to complete subsequent rounds of infection. Single-cycle SIV (scSIV) was produced by using a two-plasmid system specifically designed to minimize the possibility of generating replication-competent virus by recombination or nucleotide reversion. One plasmid carried a full-length SIV genome with three nucleotide substitutions in the gag-pol frameshift site to inactivate Pol expression. To ensure inactivation of Pol and to prevent the recovery of wild-type virus by nucleotide reversion, deletions were also introduced into the viral pol gene. In order to provide Gag-Pol in trans, a Gag-Pol-complementing plasmid that included a single nucleotide insertion to permanently place gag and pol in the same reading frame was constructed. We also mutated the frameshift site of this Gag-Pol expression construct so that any recombinants between the two plasmids would remain defective for replication. Cotransfection of both plasmids into 293T cells resulted in the release of Gag-Pol-complemented virus that was capable of one round of infection and one round of viral gene expression but was unable to propagate a spreading infection. The infectivity of scSIV was limited by the amount of Gag-Pol provided in trans and was dependent on the incorporation of a functional integrase. Single-cycle SIV produced by this approach will be useful for addressing questions relating to viral dynamics and viral pathogenesis and for evaluation as an experimental AIDS vaccine in rhesus macaques.
Modification of Structure and Magnetic Properties in Coordination Assemblies Based on [Cu(cyclam)]2+ and [W(CN)8]3−

The 1D {[CuII(cyclam)]3[WV(CN)8]2.5H2O}n (1·5H2O) (cyclam = 1,4,8,11-tetraazacyclotetradecane) coordination polymer of ladder topology can be obtained in water-alcohol solution from [Cu(cyclam)]2+ and [W(CN)8]3− building blocks. Upon dehydration, 1·5H2O undergoes a single-crystal-to-single-crystal structural transformation to the anhydrous {[CuII(cyclam)]3[WV(CN)8]2}n (1) form, which retains the same topology, but is characterized by shorter Cu-W distances and significantly more bent CN-bridges. The deformation of the coordination skeleton is reflected in magnetic properties: the predominant intra-chain interactions change from ferromagnetic in 1·5H2O to antiferromagnetic in 1. The reaction between the same building blocks in water solution under slow diffusion conditions leads to the formation of a 0D {[CuII(cyclam)(H2O)]2[CuII(cyclam)][WV(CN)8]2}. 3H2O pentanuclear assembly (2·3H2O).
Imaging Surface Immobilization Chemistry: Correlation with Cell Patterning on Non‐Adhesive Hydrogel Thin Films

High‐fidelity surface functional group (e.g., N‐hydroxysuccinimide (NHS) reactive ester) patterning is readily and reliably achieved on commercial poly(ethylene glycol) (PEG)‐based polymer films already known to exhibit high performance non‐fouling properties in full serum and in cell culture conditions. NHS coupling chemistry co‐patterned with methoxy‐capped PEG using photolithographic methods is directly spatially imaged using imaging time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) and principal components statistical analysis. Patterned NHS surface reactive zones are clearly resolved at high sensitivity despite the complexity of the polymer matrix chemistry. ToF‐SIMS imaging also reveals the presence of photo‐resist residue remaining from typical photolithography processing methods. High cross‐correlation between various ion‐derived ToF‐SIMS images is observed, providing sensitive chemical corroboration of pattern chemistry and biological reactivity in complex milieu. Surface‐specific protein coupling is observed first by site‐selective reaction of streptavidin with NHS patterns, followed by identical patterns of biotinylated Alexa‐labeled albumin coupling. This suggests that streptavidin immobilized on the patterns remains bioactive. Fluorescently labeled full serum is shown to react selectively with NHS‐reactive regions, with minimal signal from methoxy‐capped regions. Insufficient serum is adsorbed under any conditions to these surfaces to support cell attachment in serum‐containing media. This reflects the high intrinsic non‐adsorptive nature of this chemistry. Fibroblasts attach and proliferate in serum culture only when a cell adhesion peptide (RGD) is first grafted to NHS regions on the PEG‐based surfaces. Longer‐term serum‐based cell culture retains high cell‐pattern fidelity that correlates with chemical imaging of both the NHS and RGD patterns and also lack of cell adhesion to methoxy‐capped regions. Cell staining shows orientation of adherent cells within the narrow patterned areas. Cell patterns are consistently retained beyond 15 days in serum media.
Improved lexical tree search for large vocabulary speech recognition

This paper describes some extensions to the language model (LM) look-ahead pruning approach which is integrated into the time-synchronous beam search algorithm. The search algorithm is based on a lexical prefix tree in combination with a word-conditioned dynamic search space organization for handling trigram language models in a one-pass strategy. In particular, we study several LM look-ahead pruning techniques. Further, we improve the efficiency of this look-ahead technique by exploiting subtree dominance. This method avoids the computation of redundant subtrees within the copies of the lexical prefix tree and thus reduces the memory requirements of the search algorithm. In addition, we present a pruning criterion depending on the state index. The experimental results on the 20000-word NAB'94 task (ARPA North American Business Corpus) indicate that the computational effort can be reduced to 4 times real time on a ALPHA5000 PC without a significant loss in the recognition accuracy.
Series Divisions of Research & Statistics and Monetary Affairs Federal Reserve Board , Washington , D . C . The Role of the Securitization Process in the Expansion of Subprime Credit

We analyze the structure and attributes of subprime mortgage-backed securitization deals originated between 1997 and 2007. Our data set allows us to link loan-level data for over 6.7 million subprime loans to the securitization deals into which the loans were sold. We show that the securitization process, including the assignment of credit ratings, provided incentives for securitizing banks to purchase loans of poor credit quality in areas with high rates of house price appreciation. Increased demand from the secondary mortgage market for these types of loans appears to have facilitated easier credit in the primary mortgage market. To test this hypothesis, we identify an event which represents an external shock to the relative demand for subprime mortgages in the secondary market. We show that following the SEC’s adoption of rules reducing capital requirements on certain broker dealers in 2004, five large deal underwriters disproportionately increased their purchasing activity relative to competing underwriters in ZIP codes with the highest realized rates of house price appreciation but lower average credit quality. We show that these loans subsequently defaulted at marginally higher rates. Finally, using the event as an instrument, we demonstrate a causal link between the demand for mortgages in the secondary mortgage market and the supply of subprime credit in the primary mortgage market. Journal of Economic Literature classification numbers: G21, G24.
Phase transitions for gauge theories on tori from the AdS/CFT correspondence

The vacuum of a large-N gauge field on a p-torus has a spatial stress tensor with tension along the direction of smallest periodicity and equal pressures (but p times smaller in magnitude) along the other directions, assuming an AdS/CFT correspondence and a refined form of the Horowitz-Myers positive-energy conjecture. For infinite N, the vacuum exhibits a phase transition when the lengths of the two shortest periodicities cross. A comparison is made with the Surya-Schleich-Witt phase transition at finite temperature. A zero-loop approximation is also given for large but finite N.
Oxidative Processing of Latent Fas in the Endoplasmic Reticulum Controls the Strength of Apoptosis

ABSTRACT We recently demonstrated that S-glutathionylation of the death receptor Fas (Fas-SSG) amplifies apoptosis (V. Anathy et al., J. Cell Biol. 184:241–252, 2009). In the present study, we demonstrate that distinct pools of Fas exist in cells. Upon ligation of surface Fas, a separate pool of latent Fas in the endoplasmic reticulum (ER) underwent rapid oxidative processing characterized by the loss of free sulfhydryl content (Fas-SH) and resultant increases in S-glutathionylation of Cys294, leading to increases of surface Fas. Stimulation with FasL rapidly induced associations of Fas with ERp57 and glutathione S-transferase π (GSTP), a protein disulfide isomerase and catalyst of S-glutathionylation, respectively, in the ER. Knockdown or inhibition of ERp57 and GSTP1 substantially decreased FasL-induced oxidative processing and S-glutathionylation of Fas, resulting in decreased death-inducing signaling complex formation and caspase activity and enhanced survival. Bleomycin-induced pulmonary fibrosis was accompanied by increased interactions between Fas-ERp57-GSTP1 and S-glutathionylation of Fas. Importantly, fibrosis was largely prevented following short interfering RNA-mediated ablation of ERp57 and GSTP. Collectively, these findings illuminate a regulatory switch, a ligand-initiated oxidative processing of latent Fas, that controls the strength of apoptosis.
Adhesion and sliding tribological properties of polyolefins treated by diffuse coplanar surface barrier discharges

A study is presented on the plasma treatment of two different ultra-high molecular weight polyethylene (UHMW-PE) and polypropylene (PP) surfaces by using diffuse coplanar surface barrier discharges under atmospheric air conditions. The plasma-treated polymer surfaces are characterized in terms of wettability, surface chemistry, topography, adhesion and tribology. It is found that plasma treatment significantly improves wettability through formation of various oxygen containing functionalities at the surface. The plasma treatment consequently improves adhesion for either polymer/polymer or polymer/steel joints. Under dry sliding conditions the coefficient of friction slightly increases after plasma treatment in parallel with the higher adhesion. In contrast, the coefficient of friction significantly decreases under oil lubrication conditions and it remains low even after cleaning the oil likely due to the improved oil retention capability of the plasma-treated surface. The observed tendencies in adhesion and friction are further analyzed in terms of surface chemistry after plasma treatment and after sliding by use of spectroscopic methods and chemical imaging.
Treatment outcomes with long acting octreotide in inoperable hepatocellular carcinoma: a local experience and review of literature.

OBJECTIVE To determine the efficacy of long acting octreotide (LAR) in the treatment of inoperable hepatocellular carcinoma; as well as to estimate the improvement in the quality of life. METHODS This study was carried out at the Shifa International Hospital, Islamabad between February and September 2003. Patients were recruited after an informed consent. There were 22 patients who decided to take the medication whereas 20 patients refused due to socio-economic issues. They served as controls. The patients agreeable for treatment were administered octreotide 100 mcg subcutaneously thrice daily for two weeks. This was followed by monthly administration of 20 mg intramuscular octreotide. The patients were followed up for 6 months. Tumor size, alpha-fetoprotein levels, and improvement in quality of life (QOL) were monitored during therapy. RESULTS Out of 22 patients, 19 patients completed the treatment. All were males. Mean age at presentation was 55 years. Tumor size regression was seen in 10 out of 22 patients (45.5%). Mean alpha-fetoprotein levels decreased in 11 out of 22 (50%) patients. An improvement in the quality of life was seen in 10 out of 22 (45.5%) patients after treatment with long acting octreotide. In the treatment arm, 14 out of 22 (64%) patients were alive at the end of six months as compared to 10 out of 20 (50%) in the control group. CONCLUSION LAR causes tumor size regression, decreases AFP levels and improves quality of life in patients with inoperable hepatocellular carcinoma.
Incremental Tree Substitution Grammar for Parsing and Sentence Prediction

In this paper, we present the first incremental parser for Tree Substitution Grammar (TSG). A TSG allows arbitrarily large syntactic fragments to be combined into complete trees; we show how constraints (including lexicalization) can be imposed on the shape of the TSG fragments to enable incremental processing. We propose an efficient Earley-based algorithm for incremental TSG parsing and report an F-score competitive with other incremental parsers. In addition to whole-sentence F-score, we also evaluate the partial trees that the parser constructs for sentence prefixes; partial trees play an important role in incremental interpretation, language modeling, and psycholinguistics. Unlike existing parsers, our incremental TSG parser can generate partial trees that include predictions about the upcoming words in a sentence. We show that it outperforms an n-gram model in predicting more than one upcoming word.
Associations between alcohol dehydrogenase genes and alcohol use across early and middle adolescence: Moderation × Preventive intervention

Abstract Data from the in-school sample of the PROSPER preventive intervention dissemination trial were used to investigate associations between alcohol dehydrogenase genes and alcohol use across adolescence, and whether substance misuse interventions in the 6th and 7th grades (targeting parenting, family functioning, social norms, youth decision making, and peer group affiliations) modified associations between these genes and adolescent use. Primary analyses were run on a sample of 1,885 individuals and included three steps. First, we estimated unconditional growth curve models with separate slopes for alcohol use from 6th to 9th grade and from 9th to 12th grade, as well as the intercept at Grade 9. Second, we used intervention condition and three alcohol dehydrogenase genes, 1B (ADH1B), 1C (ADH1C), and 4 (ADH4) to predict variance in slopes and intercept. Third, we examined whether genetic influences on model slopes and intercepts were moderated by intervention condition. The results indicated that the increase in alcohol use was greater in early adolescence than in middle adolescence; two of the genes, ADH1B and ADH1C, significantly predicted early adolescent slope and Grade 9 intercept, and associations between ADH1C and both early adolescent slope and intercept were significantly different across control and intervention conditions.
Blood Group, Immunity, and Risk of Infection with Vibrio cholerae in an Area of Endemicity

ABSTRACT Individuals with blood group O are more susceptible than other individuals to severe cholera, although the mechanism underlying this association is unknown. To assess the respective roles of both intrinsic host factors and adaptive immune responses that might influence susceptibility to infection with Vibrio cholerae, we prospectively followed a cohort of household contacts of patients with cholera in Bangladesh. In this study, we made the novel observation that persons with blood group O were less likely than those with other blood groups to become infected with V. cholerae O1 (odds ratio [OR], 0.67; 95% confidence interval [CI], 0.53 to 0.85; P = 0.008). Consistent with prior studies, however, household contacts with blood group O were more likely to develop severe illness if infected with V. cholerae O1 (OR, 2.3; 95% CI, 0.98 to 5.59; P = 0.05). While blood group O protected significantly against infection with V. cholerae O1, there was no evidence of protection against V. cholerae O139. A multivariate analysis demonstrated that the association between blood group O and protection from infection with V. cholerae O1 was independent of age, gender, and baseline anti-cholera toxin and vibriocidal antibody titers. Based on this epidemiologic evidence, we propose a hypothesis for understanding the association between blood group O and the risk of infection with V. cholerae O1 and O139 as well as the risk of developing severe symptoms once infected.
Fe and C co-limitation of heterotrophic bacteria in the naturally fertilized region off the Kerguelen Islands

Abstract. It has been univocally shown that iron (Fe) is the primary limiting nutrient for phytoplankton metabolism in high-nutrient, low-chlorophyll (HNLC) waters, yet the question of how this trace metal affects heterotrophic microbial activity is far less understood. We investigated the role of Fe for bacterial heterotrophic production and growth at three contrasting sites in the naturally Fe-fertilized region east of the Kerguelen Islands and at one site in HNLC waters during the KEOPS2 (Kerguelen Ocean and Plateau Compared Study 2) cruise in spring 2011. We performed dark incubations of natural microbial communities amended either with iron (Fe, as FeCl3) or carbon (C, as trace-metal clean glucose), or a combination of both, and followed bacterial abundance and heterotrophic production for up to 7 days. Our results show that single and combined additions of Fe and C stimulated bulk and cell-specific bacterial production at the Fe-fertilized sites, while in HNLC waters only combined additions resulted in significant increases in these parameters. Bacterial abundance was enhanced in two out of the three experiments performed in Fe-fertilized waters but did not respond to Fe or C additions in HNLC waters. Our results provide evidence that both Fe and C are present at limiting concentrations for bacterial heterotrophic activity in the naturally fertilized region off the Kerguelen Islands in spring, while bacteria were co-limited by these elements in HNLC waters. These results shed new light on the role of Fe in bacterial heterotrophic metabolism in regions of the Southern Ocean that receive variable Fe inputs.