Miracle-dz/UniFAR-FTUs huggingface dataset:
Enforcing Consistent Translation of German Compound Coreferences

Coreferences to a German compound (e.g. Nordwand) can be made using its last constituent (e.g. Wand). Intuitively, both coreferences and the last constituent of the compound should share the same translation. However, since Statistical Machine Translation (SMT) systems translate at sentence level, they both may be translated inconsistently across the document. Several studies focus on document level consistency, but mostly in general terms. This paper presents a method to enforce consistency in this particular case. Using two in-domain phrase-based SMT systems, we analyse the effects of compound coreference translation consistency on translation quality and readability of documents. Experimental results show that our method improves correctness and consistency of those coreferences as well as document readability.
Models of Eucalypt phenology predict bat population flux

Abstract Fruit bats (Pteropodidae) have received increased attention after the recent emergence of notable viral pathogens of bat origin. Their vagility hinders data collection on abundance and distribution, which constrains modeling efforts and our understanding of bat ecology, viral dynamics, and spillover. We addressed this knowledge gap with models and data on the occurrence and abundance of nectarivorous fruit bat populations at 3 day roosts in southeast Queensland. We used environmental drivers of nectar production as predictors and explored relationships between bat abundance and virus spillover. Specifically, we developed several novel modeling tools motivated by complexities of fruit bat foraging ecology, including: (1) a dataset of spatial variables comprising Eucalypt‐focused vegetation indices, cumulative precipitation, and temperature anomaly; (2) an algorithm that associated bat population response with spatial covariates in a spatially and temporally relevant way given our current understanding of bat foraging behavior; and (3) a thorough statistical learning approach to finding optimal covariate combinations. We identified covariates that classify fruit bat occupancy at each of our three study roosts with 86–93% accuracy. Negative binomial models explained 43–53% of the variation in observed abundance across roosts. Our models suggest that spatiotemporal heterogeneity in Eucalypt‐based food resources could drive at least 50% of bat population behavior at the landscape scale. We found that 13 spillover events were observed within the foraging range of our study roosts, and they occurred during times when models predicted low population abundance. Our results suggest that, in southeast Queensland, spillover may not be driven by large aggregations of fruit bats attracted by nectar‐based resources, but rather by behavior of smaller resident subpopulations. Our models and data integrated remote sensing and statistical learning to make inferences on bat ecology and disease dynamics. This work provides a foundation for further studies on landscape‐scale population movement and spatiotemporal disease dynamics.
Rapid changes in root hydraulic conductivity and aquaporin expression in rice (Oryza sativa L.) in response to shoot removal - xylem tension as a possible signal.

BACKGROUND AND AIMS It is not clear how plants adjust the rate of root water uptake to that of shoot water loss. The aim of this study on rice was to test the idea that root aquaporins (AQPs) and xylem tension play a role in this adjustment. METHODS Three-week-old rice (Oryza sativa L.) plants, which were grown hydroponically, had their entire shoot system removed, and root hydraulic conductivity (exudation analyses) and gene expression (quantitative real-time PCR) of root plasma membrane intrinsic aquaporin proteins (PIPs) was followed within 60 min after shoot excision. KEY RESULTS All three PIP1 genes (OsPIP1;1, OsPIP1;2 and OsPIP1;3) and three of the six PIP2 genes tested (OsPIP2;1, OsPIP2;4 and OsPIP2;5) showed a rapid (5 min) and lasting (60 min) decrease in gene expression. Expression decreased by up to 85 % within 60 min. The other three PIP2 genes tested (OsPIP2;2, OsPIP2;3 and OsPIP2;6) showed a varied response, with expression decreasing either only initially (5 min) or after 60 min, or not changing at all. In a follow-up experiment, plants had their shoot system removed and the detached root system immediately connected to a vacuum pump through which some tension (80 kPa) was applied. This application of tension prevented any significant decrease in PIP expression. CONCLUSIONS Shoot removal leads to a rapid decrease in expression of all PIP1s and some PIP2s in roots of rice. Xylem tension plays some role in this process.
Proton beam monitor chamber calibration

The first goal of this paper is to clarify the reference conditions for the reference dosimetry of clinical proton beams. A clear distinction is made between proton beam delivery systems which should be calibrated with a spread-out Bragg peak field and those that should be calibrated with a (pseudo-)monoenergetic proton beam. For the latter, this paper also compares two independent dosimetry techniques to calibrate the beam monitor chambers: absolute dosimetry (of the number of protons exiting the nozzle) with a Faraday cup and reference dosimetry (i.e. determination of the absorbed dose to water under IAEA TRS-398 reference conditions) with an ionization chamber. To compare the two techniques, Monte Carlo simulations were performed to convert dose-to-water to proton fluence. A good agreement was found between the Faraday cup technique and the reference dosimetry with a plane-parallel ionization chamber. The differences—of the order of 3%—were found to be within the uncertainty of the comparison. For cylindrical ionization chambers, however, the agreement was only possible when positioning the effective point of measurement of the chamber at the reference measurement depth—i.e. not complying with IAEA TRS-398 recommendations. In conclusion, for cylindrical ionization chambers, IAEA TRS-398 reference conditions for monoenergetic proton beams led to a systematic error in the determination of the absorbed dose to water, especially relevant for low-energy proton beams. To overcome this problem, the effective point of measurement of cylindrical ionization chambers should be taken into account when positioning the reference point of the chamber. Within the current IAEA TRS-398 recommendations, it seems advisable to use plane-parallel ionization chambers—rather than cylindrical chambers—for the reference dosimetry of pseudo-monoenergetic proton beams.
Deep learning for prioritizing and responding to intrusion detection alerts

Network intrusion detection systems are widely deployed to detect cyberattacks against computer networks. These systems generate large numbers of security alerts that require manual review by security analysts to determine the appropriate courses of action required. The review of these security alerts is time consuming and can cause fatigue for security analysts, especially during long work shifts. This paper reviews a case study of the application of machine learning to the initial triage of security alerts to help reduce the manual burden placed on Department of Defense (DOD) cyber defense security analysts. This study implemented a Federated Analysis Security Triage Tool prototype. The FASTT prototype attempted to highlight, summarize and categorize tens of thousands of daily alerts/events. The prototype integrated a number of tools including TensorFlow deep neural network classifier, Elasticsearch and Kibana to provide an alternative approach for cyber defense analysts. FASTT provides a quick way to perform security alert reviews, speed up analyst queries/response, and to semi-automate threat intelligence reporting. The results of this study were evaluated for accuracy and usability. Results demonstrated that the accuracy of a deep neural network classifier was very high, as it was able to determine the heuristics that the cyber defense security analysts used in their review. Demonstrations and interviews with the security analysts showed that the prototype was able to quickly categorize security alerts into meaningful categories, provide fast query of the alerts, and save time in generating reports. Lastly, FASTT was able to pull the necessary information to generate Indications of Compromise (IOC) in a STIX/TAXII format that could be shared across DOD and US Government.
Surgical infants on total parenteral nutrition have impaired cytokine responses to microbial challenge.

BACKGROUND/PURPOSE Cytokines are essential for the prevention of microbial infections. Total parenteral nutrition (TPN) in infancy is associated with an increased risk of infection, and this could be related to altered cytokine production. The aim of the study was to determine if cytokine production is altered in monocytes from surgical infants receiving TPN. METHODS There were 3 study groups: (a) infants receiving TPN, (b) enterally fed healthy control infants, and (c) enterally fed healthy control adults. Blood samples were incubated with either Escherichia coli LPS, Staphylococcus epidermidis, or with medium alone. Flow cytometry was used to measure monocyte intracellular cytokine: tumor necrosis factor (TNF)-alpha, interleukin (IL)-6, IL-1beta. RESULTS After LPS stimulation, the percent of monocytes producing TNF-alpha and IL-6 were lower in infants on TPN than both control infants and adults. This was most apparent for TNF-alpha. The difference for IL-1beta was significant only between infant on TPN and control adults. When blood was stimulated with S. epidermidis, all 3 cytokines were significantly lower in the TPN group compared with control adults. However, the differences between infants on TPN and infant controls only reached statistical significance for IL-6. CONCLUSIONS The inflammatory response to bacterial challenge is impaired in infants on TPN compared with enterally fed infants or adults. The pattern of this response may be dependent on the nature of the microbial challenge. Our results indicate that the susceptibility of TPN-fed surgical infants to bacterial infections may in part be caused by impaired cytokine responses after bacterial invasion.
THE ROLE OF EARNINGS AND BOOK VALUES IN PRICING STOCKS : EVIDENCE FROM TURKEY

In this study, we examine factors associated with equity valuation in a newly emerging market, Turkey. In the United States and other developed countries, research indicates that both earnings and book value are important predictors of equity valuation. In Turkey, earnings appears to have information content but earnings, by itself, appears to be declining in importance over time. Book value adjusted for inflation has a stronger association with equity values. In the inflationary and risky environment of Turkey, where future value of earnings is quite uncertain, investors may be paying less attention to earnings and more attention to book values. With respect to the role of book value there are competing explanations. While some researchers conclude that it is only important because it is a control for scale differences, (Barth and Kallapur 1996) others conclude that it is relevant as a proxy for normal earnings (Ohlson 1995). Still others conclude that it is only relevant in the valuation of loss making and generally unsuccessful firms (Berger, Ofek and Swary 1997; Burgstahler and Dichev 1997). The additional contribution of this study is to show that book value is also important as a value proxy for firms operating in environments where there is rampant inflation. Our study also indicates that, overall, earnings and inflation-adjusted book values combined virtually explain almost 75 percent of the variation in equity prices in Turkey.
Dextran sulphate sodium increases splenic Gr1+CD11b+ cells which accelerate recovery from colitis following intravenous transplantation

While Gr1+CD11b+ cells are known to regulate immune responses and accumulate in most cancer tissues, the function of Gr1+CD11b+ cells in inflammation is poorly understood. We investigated the role of Gr1+CD11b+ cells in a dextran sulphate sodium (DSS)‐treated mouse model of ulcerative colitis (UC). C57BL/6 mice were treated with 2% DSS in drinking water for 5 days. Disease progression and recovery were assessed by body weight, disease activity index score (DAI) score and colon length. Splenic Gr1+CD11b+ cell number was greatly increased during the recovery phase of DSS‐induced colitis. DSS‐derived splenic Gr1+CD11b+ cells were administered intravenously to recipient (C57BL/6) mice during the early phase of DSS treatment. The transplanted splenic DSS‐induced Gr1+CD11b+ cells improved DSS‐induced colitis and promoted efficient colonic mucosal healing. We found that the CD11b+ single positive cells increased in the course of DSS‐induced colitis in lamina propria. The transplantation of splenic Gr1+CD11b+ cells induced feedback suppression of myeloid‐lineage cell development. Namely, the transplantation of splenic Gr1+CD11b+ cells greatly suppressed the migration of CD11b+ single positive cells to the lamina propria. Further, transplantation of Gr‐1+CD11b+ cells greatly suppressed the increase of the same population, especially during the late phase of DSS colitis both in spleen and bone marrow.
Selective vulnerability of preterm white matter to oxidative damage defined by F2‐isoprostanes

Periventricular white matter injury (PWMI) is the leading cause of cerebral palsy and chronic neurological disability in survivors of prematurity. Despite the large number of affected children, the pathogenetic mechanisms related to PWMI remain controversial. Through studies of 33 human autopsy brains, we determined that early PWMI was related to oxidative damage that particularly targeted the oligodendrocyte lineage, whereas other neuronal and glial cell types were markedly more resistant. F2‐isoprostanes, an arachidinate metabolite/lipid peroxidation marker of oxidative damage, were significantly increased in early PWMI lesions but not in cerebral cortex. That deleterious lipid peroxidation accompanied early PWMI was supported by similar increases in F2‐isoprostanes levels in the cerebral cortex from term infants with hypoxic‐ischemic cortical injury. Detection of F4‐neuroprostanes, a neuronal‐specific oxidative damage marker, confirmed that neuroaxonal elements were resistant to injury in cerebral cortex and white matter. Significant protein nitration was not detected in PWMI lesions by 3‐nitrotyrosine staining. Significant cellular degeneration was confirmed in early PWMI lesions by terminal deoxynucleotidyltransferase–mediated dUTP nick end labeling and a marked depletion of oligodendrocyte progenitors of 71 ± 8%. Hence, the predilection of preterm infants for PWMI is related to selective lipid peroxidation–mediated injury of cerebral white matter and targeted death of oligodendrocyte progenitors. Ann Neurol 2005;58:108–120
Imatinib Mesylate Versus Allogeneic Hematopoietic Stem Cell Transplantation for Patients with Chronic Myelogenous Leukemia.

PURPOSE To compare the relative merits of imatinib and allogeneic hematopoietic stem cell transplantation (allo-HSCT) for chronic myelogenous leukemia (CML). MATERIALS AND METHODS This cohort study was designed to compare the outcomes of imatinib (n=292) versus allo-HSCT (n=141) for CML, the clinical data of these patients being retrospectively analyzed so as to compare the event free survival (EFS) and overall survival (OS) between these two groups with patients in the chronic phase (CP) and advanced phases, including accelerate (AP) and blast phases (BP). RESULTS (1) Patients treated with imatinib (278 in the CP) demonstrated superior EFS, OS, 5-year EFS and 5-year OS rates of 88.5% versus 70.0% (P<0.05), 93.2% versus 80.0% (P<0.05), 84% versus 75.0% (P<0.05) and 92% versus 79.0% (P<0.05), respectively, to those treated with allo-HSCT (120 patients in the CP). (2) Both treatments resulted in similar survival, with EFS and OS rates of 42.9% versus 47.6% (P>0.05), 42.9% versus 57.1% (P>0.05), respectively, for imatinib (14 patients in the AP and BP) and allo-HSCT (21 patients in the AP and BP). CONCLUSIONS Imatinib confers signi cant survival advantage (EFS and OS) for CML patients with CP compared with allo-HSCT treatment. However, the outcomes are equally good with both treatments in AP and BP patients.
Optimization of light sources for prostate photodynamic therapy

To deliver uniform photodynamic dose to the prostate gland, it is necessary to develop algorithms that optimize the location and strength (emitted power × illumination time) of each light source. Since tissue optical properties may change with time, rapid (almost real-time) optimization is desirable. We use the Cimmino algorithm because it is fast, linear, and always converges reliably. A phase I motexafin lutetium (MLu)-mediated photodynamic therapy (PDT) protocol is on-going at the University of Pennsylvania. The standard plan for the protocol uses equal source strength and equal spaced loading (1-cm). PDT for the prostate is performed with cylindrical diffusing fibers (CDF) of various lengths inserted to longitudinal coverage within the matrix of parallel catheters perpendicular to a base plate. We developed several search procedures to aid the user in choosing the positions, lengths, and intensities of the CDFs. The Cimmino algorithm is used in these procedures to optimize the strengths of the light catheters at each step of the iterative selection process. Maximum and minimum bounds on allowed doses to points in four volumes (prostate, urethra, rectum, and background) constrain the solutions for the strengths of the linear light sources. Uniform optical properties are assumed. To study how different opacities of the prostate would affect optimization, optical kernels of different light penetration were used. Another goal is to see whether the urethra and rectum can be spared, with minimal effect on PTV treatment delivery, by manipulating light illumination times of the sources. Importance weights are chosen beforehand for organ volumes, and normalized. Compared with the standard plan, our algorithm is shown to produce a plan that better spares the urethra and rectum and is very fast. Thus the combined selection of positions, lengths, and strengths of interstitial light sources improves outcome.
Characterization of the Chromosomal Binding Sites andDimerization Partners of the Viral Oncoprotein Meq in Marek'sDisease Virus-Transformed TCells

ABSTRACT Marek's disease virus (MDV) is an acute transforming alphaherpesvirus that causes T-cell lymphomas in chickens. We previously reported the identification of a putative oncogene, meq, that is encoded only by the oncogenic serotype of MDV. The gene product, Meq, is a latent protein that is consistently expressed in MDV-transformed lymphoblastoid cells and tumor cells. Meq has a bZIP (basic leucine zipper) structure resembling the family of Jun/Fos. The mechanism whereby Meq transforms T cells remains poorly understood. In this study, we explored the properties of Meq as a transcriptional factor. We analyzed Meq's dimerization partners and its target genes in MSB-1, an MDV-transformed T-cell line. By using in vitro assays, we first demonstrated Meq's potential to dimerize with a variety of bZIP proteins. We then identified c-Jun as the primary dimerization partner of Meq. Both are found to be colocalized in the nucleus and corecruited to promoters with AP-1 sequences. By using chromatin immunoprecipitation (ChIP), we scanned the entire MDV genome for Meq binding sites and found three regions that were enriched with Meq binding: the MDV lytic replication origin, the promoter for Meq, and the promoter for ICP4. Transactivation assays using the above promoters showed that Meq/Meq homodimers exhibited repression activity, whereas Meq/Jun heterodimers showed activation. Finally, we were able to show by ChIP that Meq is recruited to the interleukin-2 promoter in a region encompassing an AP-1 site. Thus, in addition to providing general knowledge about the transcriptional properties of Meq, our studies revealed for the first time the ability of Meq to interact with the latent MDV and host genomes. Our data suggest, therefore, a role for Meq in viral genome regulation during latency, in addition to its putative causal role in T-cell transformation.
Impact of butyrate on microbial selection in enhanced biological phosphorus removal systems

Microbial selection in an enhanced biological phosphorus removal system was investigated in a laboratory-scale sequencing batch reactor fed exclusively with butyrate as a carbon source. As reported in the few previous studies, butyrate uptake was slow and phosphorus (P) release occurred during the entire anaerobic period. Polyphosphate-accumulating organism (PAO), i.e. Candidatus Accumulibacter phosphatis (named as Accumulibacter), glycogen-accumulating organisms (GAOs), i.e. Candidatus Competibacter phosphatis (named as Competibacter) and Defluviicoccus-related, tetrad-forming alphaproteobacteria (named as Defluviicoccus) were identified using fluorescence in situ hybridization analysis. The results show that Accumulibacter and Defluviicoccus were selected in the butyrate-fed reactor, whereas Competibacter was not selected. P removal was efficient at the beginning of the experiment with an increasing percentage relative abundance (% RA) of PAOs. The % RA of Accumulibacter and Defluviicoccus increased from 13% to 50% and 8% to 16%, respectively, and the % RA of Competibacter decreased from 8% to 2% during the experiment. After 6 weeks, P removal deteriorated with the poor correlation between the percentage of P removal and % RA of GAOs.
Bacteremia in Diabetic Patients: Comparison of Incidence and Mortality with Nondiabetic Patients

We determined the incidence of bacteremia and associated mortality in diabetic and nondiabetic patients in the four major hospitals of one metropolitan area over the 5-yr period 1977–1981. Mortality rates, based on episodes of bacteremia, were similar in diabetic and nondiabetic patients in most instances. Diabetic patients experienced lower mortality rates from Enterobacteriaceae bacteremia compared with nondiabetic patients; this finding was explained by a greater tendency for diabetic patients to have Escherichia coli bacteremia due to community-acquired urinary tract infection. However, the incidence of bacteremia due to all microorganisms was increased twofold in diabetic patients and the incidence of Enterobacteriaceae bacteremia was increased threefold. Because of their increased incidence of bacteremia, diabetic patients in this population were nearly twice as likely to die as a result of bacteremia compared with nondiabetic patients. Thus, the frequent occurrence of bacteremia among patients with diabetes mellitus represents a significant problem.
A decision theoretical modeling for Phase III investments and drug licensing

ABSTRACT For a new candidate drug to become an approved medicine, several decision points have to be passed. In this article, we focus on two of them: First, based on Phase II data, the commercial sponsor decides to invest (or not) in Phase III. Second, based on the outcome of Phase III, the regulator determines whether the drug should be granted market access. Assuming a population of candidate drugs with a distribution of true efficacy, we optimize the two stakeholders’ decisions and study the interdependence between them. The regulator is assumed to seek to optimize the total public health benefit resulting from the efficacy of the drug and a safety penalty. In optimizing the regulatory rules, in terms of minimal required sample size and the Type I error in Phase III, we have to consider how these rules will modify the commercial optimization made by the sponsor. The results indicate that different Type I errors should be used depending on the rarity of the disease.