Miracle-dz/UniFAR-FTUs huggingface dataset:
Syntactic Tree-based Relation Extraction Using a Generalization of Collins and Duffy Convolution Tree Kernel

Relation extraction is a challenging task in natural language processing. Syntactic features are recently shown to be quite effective for relation extraction. In this paper, we generalize the state of the art syntactic convolution tree kernel introduced by Collins and Duffy. The proposed generalized kernel is more flexible and customizable, and can be conveniently utilized for systematic generation of more effective application specific syntactic sub-kernels. Using the generalized kernel, we will also propose a number of novel syntactic sub-kernels for relation extraction. These kernels show a remarkable performance improvement over the original Collins and Duffy kernel in the extraction of ACE-2005 relation types.
Combining ability and testcross performance of drought‐tolerant maize inbred lines under stress and non‐stress environments in Kenya

Abstract Drought and poor soil fertility are among the major abiotic stresses affecting maize productivity in sub‐Saharan Africa. Maize breeding efforts at the International Maize and Wheat Improvement Center (CIMMYT) have focused on incorporating drought stress tolerance and nitrogen‐use efficiency (NUE) into tropical maize germplasm. The objectives of this study were to estimate the general combining ability (GCA) and specific combining ability (SCA) of selected maize inbred lines under drought stress (DS), low‐nitrogen (LN) and optimum moisture and nitrogen (optimum) conditions, and to assess the yield potential and stability of experimental hybrids under these management conditions. Forty‐nine experimental three‐way cross hybrids, generated from a 7 × 7 line by tester crosses, and six commercial checks were evaluated across 11 optimum, DS and LN sites in Kenya in 2014 using an alpha lattice design with two replicates per entry at each site. DS reduced both grain yield (GY) and plant height (PH), while anthesis–silking interval (ASI) increased under both DS and LN. Hybrids ‘L4/T2’ and ‘L4/T1’ were found to be superior and stable, while inbreds ‘L4’ and ‘L6’ were good combiners for GY and other secondary traits across sites. Additive variance played a greater role for most traits under the three management conditions, suggesting that further progress in the improvement of these traits should be possible. GY under optimum conditions was positively correlated with GY under both DS and LN conditions, but GY under DS and LN was not correlated. Our results suggest the feasibility for simultaneous improvement in grain yield performance of genotypes under optimum, DS and LN conditions.
Etiology of Ibrutinib Therapy Discontinuation and Outcomes in Patients With Chronic Lymphocytic Leukemia.

IMPORTANCE The Bruton tyrosine kinase (BTK) inhibitor ibrutinib is effective in patients with chronic lymphocytic leukemia (CLL). Reasons for discontinuing therapy with this drug and outcomes following discontinuation have not been evaluated outside of clinical trials with relatively short follow-up. OBJECTIVE To determine features associated with discontinuation of ibrutinib therapy and outcomes. DESIGN, SETTING, AND PARTICIPANTS A total of 308 patients participating in 4 sequential trials of ibrutinib at The Ohio State University Comprehensive Cancer Center were included. These clinical trials accrued patients included in this analysis from May 2010 until April 2014, and data were locked in June 2014. MAIN OUTCOMES AND MEASURES Patients were evaluated for time to therapy discontinuation, reasons for discontinuation, and survival following discontinuation. For patients who discontinued therapy because of disease progression, targeted deep sequencing was performed in samples at baseline and time of relapse. RESULTS With a median follow-up of 20 months, 232 patients remained on therapy, 31 had discontinued because of disease progression, and 45 had discontinued for other reasons. Disease progression includes Richter's transformation (RT) or progressive CLL. Richter's transformation appeared to occur early and CLL progressions later (cumulative incidence at 12 months, 4.5% [95% CI, 2.0%-7.0%] and 0.3% [95% CI, 0%-1.0%], respectively). Median survival following RT was 3.5 months (95% CI, 0.3-6.0 months) and 17.6 months (95% CI, 4.7 months-"not reached") following CLL progression. Sequencing on peripheral blood from 8 patients with RT revealed 2 with mutations in BTK, and a lymph node sample showed no mutations in BTK or PLCG2. Deep sequencing on 11 patients with CLL progression revealed BTK or PLCG2 mutations in all. These mutations were not identified before treatment in any patient. CONCLUSIONS AND RELEVANCE This single-institution experience with ibrutinib confirms it to be an effective therapy and identifies, for the first time, baseline factors associated with ibrutinib therapy discontinuation. Outcomes data show poor prognosis after discontinuation, especially for those patients with RT. Finally, sequencing data confirm initial reports associating mutations in BTK and PLCG2 with progression and clearly show that CLL progressions are associated with these mutations, while RT is likely not. TRIAL REGISTRATIONS clinicaltrials.gov Identifiers:NCT01105247, NCT01217749, NCT01589302, and NCT01578707.
Effect of UV radiation and temperature on the emission of methane from plant biomass and structural components

Abstract. The recently reported finding that plant matter and living plants produce significant amounts of the important greenhouse gas methane under aerobic conditions has led to an intense scientific and public controversy. Whereas some studies question the up-scaling method that was used to estimate the global source strength, others have suggested that experimental artifacts could have caused the reported signals, and two studies, one based on isotope labeling, have recently reported the absence of CH4 emissions from plants. Here we show – using several independent experimental analysis techniques – that dry and detached fresh plant matter, as well as several structural plant components, emit significant amounts of methane upon irradiation with UV light and/or heating. Emissions from UV irradiation are almost instantaneous, indicating a direct photochemical process. Long-time irradiation experiments demonstrate that the size of the CH4 producing reservoir is large, exceeding potential interferences from degassing or desorption processes by several orders of magnitude. A dry leaf of a pure 13C plant produces 13CH4 at a similar rate as dry leaves of non-labeled plants produce non-labeled methane.
Shear-induced self-diffusion in concentrated suspensions

Suspensions consist of solid particles dispersed in a liquid. In practice they are for example used for large-scale transport of particulate materials like sand. During oil and gas drilling suspensions are utilized for the transport of rock cuttings. Furthermore they can be found in industry in the production of foods, paint and paper. Knowledge of the flow properties of suspensions is therefore of practical interest and forms an important research area in rheology. This thesis contains the results of an experimental investigation of ’shear-induced diffusion’. It is by now well-known that individual particles in concentrated suspensions of non-colloidal particles (> 10 μm) exhibit a fluctuating motion under influence of an externally applied flow field. The process can be characterized as diffusion and is caused by the fact that particles on neighbouring streamlines are forced to pass each other. The interactions are asymmetrical and lead to particle displacements.
Site Size of Cooperative Single-stranded RNA Binding by Poliovirus RNA-dependent RNA Polymerase*

The poliovirus RNA-dependent RNA polymerase binds cooperatively to single-stranded RNA. We have determined the minimal RNA-binding site size of the poliovirus polymerase using binding titration with oligonucleotides of increasing length. A dramatic increase in affinity was observed when the length of the oligo(U) increased from 8 to 10 nucleotides (nt), arguing that the minimal size of RNA for polymerase binding is 10 nt. Another increase in affinity seen as the oligo(U) reached 24 nt suggests that a 24-nucleotide RNA can be occupied by two polymerase molecules. Direct binding of wild-type polymerase to oligo(U)12 and oligo(U)24 RNAs showed differences in affinity and cooperativity consistent with this model. The increase in binding affinity seen for oligo(U)10 suggests either that the RNA-binding determinants are widely spaced on the polymerase structure or that a substantial conformational change in the polymerase occurs upon the filling of its RNA-binding site.
Apical constriction and epithelial invagination are regulated by BMP activity

ABSTRACT Epithelial invagination is a morphological process in which flat cell sheets transform into three-dimensional structures through bending of the tissue. It is accompanied by apical constriction, in which the apical cell surface is reduced in relation to the basal cell surface. Although much is known about the intra-cellular molecular machinery driving apical constriction and epithelial invagination, information of how extra-cellular signals affect these processes remains insufficient. In this study we have established several in vivo assays of placodal invagination to explore whether the external signal BMP regulates processes connected to epithelial invagination. By inhibiting BMP activity in prospective cranial placodes, we provide evidence that BMP signals are required for RhoA and F-actin rearrangements, apical constriction, cell elongation and epithelial invagination. The failure of placode invagination after BMP inhibition appears to be a direct consequence of disrupted apical accumulation of RhoA and F-actin, rather than changes in cell death or proliferation. In addition, our results show that epithelial invagination and acquisition of placode-specific identities are two distinct and separable developmental processes. In summary, our results provide evidence that BMP signals promote epithelial invagination by acting upstream of the intracellular molecular machinery that drives apical constriction and cell elongation. Summary: We describe a novel role for BMP activity in promoting a direct and cell type-independent mechanism for apical constriction, cell elongation and epithelial invagination, separate from acquisition of placode-specific identities.
Hormonal responses during prolonged exercise are influenced by a selective DA/NA reuptake inhibitor

Objective: A decrease in dopamine activity is thought to lead to a reduction in motivation and arousal and therefore to the “central” component of fatigue. The purpose of the present study was to investigate the effects of a dopamine (DA) noradrenaline (NA) reuptake inhibitor, bupropion (Zyban™), on exercise performance and on the hormonal response to exercise. Methods: Eight healthy well trained male cyclists (Wattmax 397±15 W) participated in the study. Subjects completed one maximal exercise test (to determine maximal power output Wattmax), and two endurance performance tests (time trials) in a double blind randomised cross-over design. Subjects took either placebo capsules (lactose) or 2×300 mg bupropion (BUP). Blood samples were collected for adrenocorticotropin (ACTH), prolactin, cortisol, growth hormone, beta-endorphins, and catecholamines. Results: Performance was not influenced by BUP (placebo: 89±1 min; BUP 2×300 mg: 89±0.7 min). All hormones increased during exercise in all trials. Cortisol plasma concentrations were significantly higher in the BUP trial at rest, at min 60, and at the end of exercise, while beta-endorphins were higher in the BUP trial at the end of exercise and during recovery, and ACTH at the end of exercise. Conclusion: From the present results, we can conclude that bupropion had a more marked central noradrenergic effect (compared to dopaminergic) on the hormonal response to exercise, but no effect on the outcome of performance.
A single‐center experience with 200 dual kidney transplantations

This study reports on a large series of 200 dual kidney transplantations (DKTs) from expanded criteria donors (ECDs) and proposes specific ways to optimize outcomes. Data concerning 200 DKTs performed in the last 14 yr were retrospectively analyzed. Kidneys from high‐risk ECD were allocated for use in DKTs on an old‐for‐old basis after histological assessment. Different surgical techniques and immunosuppressant regimens were used over time, and the outcomes are discussed. Donors and recipients were a median 73 (70–77) and a 62 (58–67) yr old, respectively. Delayed graft function occurred in 31.5% of cases, and acute rejection in 13.5%. Patient and graft survival at five yr were 90.4% and 85.8%, respectively. Unilateral kidney placement was preferred for 75% of patients, and was associated with a low rate of surgical complications. Our current standard therapy comprising low‐dose calcineurin inhibitors (CNIs) associated with mammalian target of rapamycin inhibitors (mTOR) and steroids appears to offer the best risk/benefit profile for elderly patients undergoing DKT. In our experience, outcomes after DKT can be improved by: (i) kidney clinical–histological assessment; (ii) unilateral kidney placement; (iii) minimal use of CNI associated with mTOR.
The Alexander Project 1996-1997: latest susceptibility data from this international study of bacterial pathogens from community-acquired lower respiratory tract infections.

The Alexander Project was established in 1992 to examine antimicrobial susceptibilities of bacterial isolates from community-acquired infections of the lower respiratory tract. Testing of a range of compounds was undertaken in a central laboratory. From 1992 to 1995, isolates were collected from geographically separated areas in countries in the European Union and various states in the USA. In 1996, the study was extended to include centres in Mexico, Brazil, Saudi Arabia, South Africa, Hong Kong and other European countries not included previously. Data generated by the project during 1996-1997 confirm France and Spain as European centres with high rates of resistance to penicillin among isolates of Streptococcus pneumoniae. Both intermediate (MIC 0. 12-1 mg/L) and resistant (MIC 2 mg/L) phenotypes are present. Combined resistance rates (intermediate and resistant) were >/=50% in 1997. Combined resistance rates in excess of 20% were found in the Republic of Ireland, Portugal, the Slovak Republic and Hungary. Penicillin resistance continues to evolve in the USA, with combined resistance rates of 16.4% (1996) and 18.6% (1997). In the new, non-European centres, e.g. Mexico and, in particular, Hong Kong (where resistant strains accounted for 50% of all isolates of S. pneumoniae in 1996 and 55.5% in 1997), there are centres where rates of resistance are high. Macrolide resistance is increasing generally among both penicillin-resistant and penicillin-susceptible isolates of S. pneumoniae. There is variation between countries, and in four out of the 16 centres for which both 1996 and 1997 data are available, rates of macrolide resistance have fallen. Overall, the percentage of S. pneumoniae strains that is resistant to macrolides exceeds the percentage that is resistant to penicillin. In 1996, 16. 5% of all S. pneumoniae isolates were resistant to macrolides compared with 10.4% resistant to penicillin, and in 1997 respective rates were 21.9% and 14.1%. beta-Lactamase production was the principal mechanism of resistance observed among isolates of Haemophilus influenzae. However, considerable variation in the percentage of isolates producing beta-lactamase (0-37.1%) was observed within this species. Within Europe, in the Republic of Ireland, France and Belgium, more than 15% of isolates were beta-lactamase producers. In Spain rates were as high as 31.7%. Outside Europe and the USA high rates were described in Mexico (25%), Saudi Arabia (27.9%, 16.7%) and Hong Kong (37.1%, 28.9%). Of H. influenzae from the USA, 30.4% were beta-lactamase producers in 1996 and 23.3% in 1997. beta-Lactamase production among isolates of Moraxella catarrhalis was observed in >90% of the isolates tested in 1996 and 1997.
Indexing Structures Derived from Syntax in TREC-3: System Description

This paper describes an approach to information retrieval based on a syntactic analysis of the document texts and user queries and from that analysis, the construction of tree structures (TSAs) to encode and capture language ambiguities. TSAs are constructed at the clause many TSAs and each query may be represented by several TSAs. The TSAs from documents and from queries are then matched and their degrees of overlap between individual TSAs are computed and then aggregated to yield a score for each document, which is then used in ranking the collection. This paper presents the system description when benchmarking our retrieval strategy on category B of TREC-3, i.e. on c.550 Mbytes of the Wall Street Journal newspaper texts. The implementation is based on a two-stage retrieval where a statistically-based pre-fetch retrieval retrieves the set of WSJ articles for the more computationnaly expensive language based processing. The results of our retrieval system in terms of precision and recall are disappointing and an analysis of why is also included. Part of this analysis includes a direct comparison between our system and some mainstream IR approaches. In addition to performaing ad hoc retrieval on texts in English, we have also performed ad hoc retrieval retrieval on texts in Spanish using a weighted trigram approach, and this is outlined and performance results given in an appendix.
Experimental evaluation of ride-through capabilities for a matrix converter under short power interruptions

The matrix converters, which are direct power electronic converters, are able to provide important benefits such as bidirectional power flow, sinusoidal input currents with adjustable displacement angle, and a great potential for size reduction. Still, two major disadvantages exist: a lower than unity voltage transfer ratio and high sensitivity to power grid disturbances. Many solutions to provide continuous operation of adjustable speed drives (ASDs) during power grid disturbances have been proposed, but they are all applied to DC-link ASD. In this paper, a new solution to provide limited ride-through operation is presented with a matrix converter using a scalar controlled induction motor for a duration of hundreds of milliseconds, without any hardware modification. During the ride-through operation, the drive is not able to develop torque or to control the motor flux. By recovering the necessary power to feed the control hardware of the matrix converter, it is able to keep the ASD operating. When normal grid conditions are reestablished, the matrix converter is able to accelerate the motor from nonzero speed and flux by initializing the modulator with the estimated frequency and the initial angle of the reference output voltage vector. The maximum duration of the ride-through operation depends on the initial motor flux, speed level, rotor time constant, load torque, and inertia. This method is verified on a laboratory setup with a matrix converter.
Hydroxytyrosol: a new class of microbicide displaying broad anti-HIV-1 activity

Objective:To investigate the toxicity and activity against HIV of 5-hydroxytyrosol as a potential microbicide. Design:The anti-HIV-1 activity of 5-hydroxytyrosol, a polyphenolic compound, was tested against wild-type HIV-1 and viral clones resistant to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors and integrase inhibitors. In addition to its activity against founder viruses, different viral subtypes and potential synergy with tenofovir disoproxil fumarate, lamivudine and emtricitabine was also tested. 5-Hydroxytyrosol toxicity was evaluated in vivo in rabbit vaginal mucosa. Methods:We have cloned pol gene from drug-resistant HIV-1 isolated from infected patients and env gene from Fiebeg III/IV patients or A, C, D, E, F and G subtypes in the NL4.3-Ren backbone. 5-Hydroxytyrosol anti-HIV-1 activity was evaluated in infections of MT-2, U87-CCR5 or peripheral blood mononuclear cells preactivated with phytohemagglutinin + interleukin-2 with viruses obtained through 293T transfections. Inhibitory concentration 50% and cytotoxic concentration 50% were calculated. Synergy was analysed according to Chou and Talalay method. In-vivo toxicity was evaluated for 14 days in rabbit vaginal mucosa. Results:5-Hydroxytyrosol inhibited HIV-1 infections of recombinant or wild-type viruses in all the target cells tested. Moreover, 5-hydroxytyrosol showed similar inhibitory concentration 50% values for infections with NRTIs, NNRTIs, protease inhibitors and INIs resistant viruses; founder viruses and all the subtypes tested. Combination of 5-hydroxytyrosol with tenofovir was found to be synergistic, whereas it was additive with lamivudine and emtricitabine. In-vivo toxicity of 5-hydroxytyrosol was very low even at the highest tested doses. Conclusion:5-Hydroxytyrosol displayed a broad anti-HIV-1 activity in different cells systems in the absent of in-vivo toxicity, therefore supporting its candidacy as a potential new class of microbicides.
PTSD symptom severity relates to cognitive and psycho-social dysfunctioning – a study with Congolese refugees in Uganda

ABSTRACT Background: In the ongoing conflict in the Democratic Republic of the Congo (DRC), civilians have been heavily exposed to traumatic stressors. Traumatizing experiences cumulatively heighten the risk for trauma-related disorders, and with it affect cognitive and psycho-social functioning. Objectives: We aimed at investigating the association between trauma-related disorders and cognitive and psycho-social functioning and hypothesized that PTSD symptom severity would negatively correlate with executive functioning, working memory and psycho-social functioning in everyday life. Method: In total, 323 Congolese refugees (mean age: 31.3 years) who arrived in the Ugandan Nakivale refugee settlement after January 2012 were assessed regarding their exposure to traumatic events, PTSD symptom severity (posttraumatic symptom scale interview), executive functioning (Tower of London), working memory performance (Corsi block tapping task) and psycho-social dysfunctioning (Luo functioning scale). Results: Hierarchical regression analyses indicated a significant negative association between PTSD symptom severity and working memory (β = –0.32, p < 0.001), as well as executive functions (β = –0.19, p = 0.003). Furthermore, the impairment of psycho-social functioning in everyday life was positively related with PTSD symptom severity (β = 0.70, p < 0.001), and negatively with executive functioning (β = –0.15, p = 0.003). However, working memory performance was not significantly related to psycho-social dysfunctioning (β = 0.09, p > 0.05). Conclusion: Trauma survivors not only suffer from the core PTSD symptoms but also from impaired cognitive functioning. PTSD symptom severity seems furthermore to be related to impaired psycho-social functioning. Our findings suggest that trauma-related mental health problems may heighten the risk for poverty and lack of prospect and further aggravate the consequences of war and conflict.