Miracle-dz/UniFAR-FTUs huggingface dataset:
The potential for calcium depletion in forest ecosystems of southeastern United States: Review and analysis

Biogeochemical mass balance assessments of calcium status in southeastern forests indicate that losses through harvesting and soil leaching often exceed inputs from atmospheric deposition and weathering. Many forest soils of the southeastern United States are particularly sensitive because these soils and the underlying saprolite from which these soils are derived are largely depleted of weatherable calcium. At most of the intensively studied sites in the southeastern United States, it is estimated that calcium depletion has already reduced or will likely reduce exchangeable soil calcium reserves to less than the estimated requirement for a merchantable forest stand in 150 years or less. At most sites, calcium uptake into merchantable wood equals or exceeds soil leaching losses. Chronic atmospheric deposition of sulfate and nitrate and declining atmospheric deposition of calcium are likely to accelerate calcium depletion. The southeastern U.S. regional distribution of soil calcium pools and calcium fluxes (deposition and uptake in merchantable wood) indicates that the depletion status of the intensively studied sites is representative of a substantially larger area. Where weathering inputs are insufficient to replace leaching and uptake losses, there is a potential for a regional problem in forest nutrition over the long term.
Protective Effects of Garlic and Silymarin on NDEA-Induced Rats Hepatotoxicity

Background — The present study was conducted to investigate the chemopreventive effects of garlic extract and silymarin on N-nitrosodiethylamine (NDEA) and carbon tetrachloride (CCl4)-induced hepatotoxicity in male albino rats. Methods and Results — Animals were pretreated with garlic, silymarin or both for one week prior to the injection of NDEA. Then animals received a single injection of NDEA followed by weekly subcutaneous injections of CCl4 for 6 weeks. Oral administration was then continued along with the injection of CCl4 for the duration of the experiment. Serum aspartate transaminase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), hepatic lipid peroxidation (LPO), superoxide dismutase (SOD), reduced glutathione (GSH), glutathione-S-transferase (GST) and glutathione reductase (GSR) were measured. Injection of NDEA induced a significant elevation in serum AST, ALT and ALP. In the liver, NDEA increased oxidative stress through the increase in LPO and decrease in SOD, and GSH-dependent enzymes. Although administration of garlic or silymarin significantly reduced the liver toxicity, combined administration was more effective in preventing the development of hepatotoxicity. Conclusion — These novel findings suggest that silymarin and garlic have a synergistic effect, and could be used as hepatoprotective agents against hepatotoxicity.
Horizontal transmission of streptococcus mutans in schoolchildren

Objetive: The aim of this study was to analyze possible horizontal transmission patterns of S. mutans among 6-7-yr-old schoolchildren from the same class, identifying genotypes and their diversity and relationship with caries disease status. Study Design: Caries indexes and saliva mutans streptococci and lactobacilli counts were recorded in 42 schoolchildren. Mutans streptococci colonies were identified by means of biochemical tests and all S. mutans strains were genotyped by arbitrarily primed polymerase chain reaction. A child was considered free of S. mutans when it could not be isolated in 3 samples at 1-week intervals. Results: S. mutans was isolated in 30 schoolchildren: 20 having one genotype and 10 two genotypes. Higher mutans streptococci and caries index values were found in those with two genotypes. Five genotypes were isolated in more than 1 schoolchild and one of these was isolated in 3 schoolchildren. Our results suggest that horizontal transmission may take place. Conclusion: Schoolchildren aged 6-7 yrs may be the source of mutual transmission of S. mutans. Key words:Streptococcus mutans, Horizontal transmission, AP-PCR, genotyping
Biofilm formation in surface and drinking water distribution systems in Mafikeng, South Africa

Poor quality source water and poorly treated reused wastewater may result in poor quality drinking water that has a higher potential to form biofilms. A biofilm is a group of microorganisms which adhere to a surface. We investigated biofilm growth in the drinking water distribution systems in the Mafikeng area, in the North- West Province of South Africa. Analysis was conducted to determine the presence of faecal coliforms, total coliforms, Pseudomonas spp. and Aeromonas spp. in the biofilms. Biofilms were grown on a device that contained copper and galvanised steel coupons. A mini tap filter – a point-of-use treatment device which can be used at a single faucet – was also used to collect samples. Scanning electron microscopy demonstrated that multi-species biofilms developed on all the coupons as well as on the point-of-use filters. Galvanised steel and carbon filters had the highest density of biofilm. Total coliforms, faecal coliforms and Pseudomonas spp. were isolated from raw water biofilm coupons only. Aeromonas spp. and Pseudomonas spp. were isolated from filters. The susceptibility of selected isolates was tested against 11 antibiotics of clinical interest. The most prevalent antibiotic resistance phenotype observed was KF-AP-C-E-OT-K-TM-A. The presence of virulence genes was determined using the polymerase chain reaction. These results indicate that bacteria present in the water have the ability to colonise as biofilms and drinking water biofilms may be a reservoir for opportunistic bacteria including Pseudomonas and Aeromonas species.
A novel methodology for adaptive Wave Filtering of marine vessels: Theory and experiments?

This paper addresses a filtering problem that arises in the design of dynamic positioning systems for ships and offshore rigs subjected to the influence of sea waves. The vessel's dynamic model adopted captures the sea state as an uncertain parameter. The proposed adaptive Wave Filtering (WF) consists of a recursive optimization procedure which seeks to identify the dominant wave frequency (the uncertain parameter) by minimizing an appropriate defined performance index. The estimated dominant wave frequency is used to identify the sea condition, based on which adaptive wave filtering (using a Kalman filter) is performed for dynamic positioning purposes. The adaptive WF enables the DP system to operate in different operational conditions and hence, it is a step forward to a so-called all-year marine DP system. The results are experimentally verified by model testing a DP operated ship, the Cybership III, under different sea conditions, in a towing tank equipped with a hydraulic wave maker.
Aggressive and protective behaviour of adult rabbits Oryctolagus cuniculus (L.) towards juveniles.

Adult wild rabbits, Oryctolagus cuniculus (L). were confronted experimentally in their own pens with o-60 day old kittens of three different descents: "own" "group" and "strangers". The ability to differentiate between kittens of these three categories was displayed by adults of both sexes and was statistically significant for a number of measures taken. Does tolerated "own" kittens but attacked "group" progeny and "strangers". The severity of aggression as measured by the incidence of biting, ripping, squealing, killing and severity of wounds was higher in relation to "strangers" than "group" kittens. Adult males tolerated young kittens irrespective of their parentage and displayed amicable behaviour-chinning and licking-towards them. However they showed a small amount of aggression towards some juveniles approaching maturity. To minimise injuries to kittens the behaviour of females had to be studied in the presence of the bucks. The protective (altruistic) role of the males demonstrated by their attacks on the females reduced the severity of the does' aggression towards the kittens. Adults identified kittens by smell, sniffing most commonly at the hindquarters and head regions in which the skin glands (chin, anal, inguinal) are located. Blindfolding of adults slowed down aggression but did not eliminate it completely and did not affect their ability to differentiate between "group" progeny and "strangers". There were individual differences in the severity of aggression by females and the protective behaviour of bucks. The aggression of adult females and the protection of males in relation to kittens are discussed generally and the important role of territoriality in inhibiting aggression in wild rabbits is emphasised.
Comparison of compression efficiency between HEVC/H.265 and VP9 based on subjective assessments

Current increasing effort of broadcast providers to transmit UHD (Ultra High Definition) content is likely to increase demand for ultra high definition televisions (UHDTVs). To compress UHDTV content, several alternative encoding mechanisms exist. In addition to internationally recognized standards, open access proprietary options, such as VP9 video encoding scheme, have recently appeared and are gaining popularity. One of the main goals of these encoders is to efficiently compress video sequences beyond HDTV resolution for various scenarios, such as broadcasting or internet streaming. In this paper, a broadcast scenario rate-distortion performance analysis and mutual comparison of one of the latest video coding standards H.265/HEVC with recently released proprietary video coding scheme VP9 is presented. Also, currently one of the most popular and widely spread encoder H.264/AVC has been included into the evaluation to serve as a comparison baseline. The comparison is performed by means of subjective evaluations showing actual differences between encoding algorithms in terms of perceived quality. The results indicate a general dominance of HEVC based encoding algorithm in comparison to other alternatives, while VP9 and AVC showing similar performance.
Short-Term Retrograde Inhibition of GABAergic Synaptic Currents in Rat Purkinje Cells Is Mediated by Endogenous Cannabinoids

Depolarization-induced suppression of inhibition (DSI) is a form of short-term plasticity of GABAergic synaptic transmission that is found in cerebellar Purkinje cells and hippocampal CA1 pyramidal cells. DSI involves the release of a calcium-dependent retrograde messenger by the somatodendritic compartment of the postsynaptic cell. Both glutamate and endogenous cannabinoids have been proposed as retrograde messenger. Here we show that, in cerebellar parasagittal slices, type 1 cannabinoid receptors (CB1Rs) are expressed at high levels in axons of GABAergic interneurons and in presynaptic terminals onto Purkinje cells. Application of the cannabinoid antagonist AM-251 (500 nm) leads to the abolition of the DSI of evoked currents (eIPSCs) recorded in paired recordings and to a strong reduction of the DSI of TTX-insensitive miniature events (mIPSCs) recorded from Purkinje cells. Furthermore, the CB1R agonist WIN 55–212,2 (5 μm) induces a presynaptic inhibition of synaptic currents similar to that occurring during DSI, as well as an occlusion of DSI after stimulation of Purkinje cells. Moreover, WIN 55–212,2 reduces the calcium transients evoked in presumed presynaptic varicosities by short trains of action potentials. Our results indicate that DSI is mediated by the activation of presynaptic CB1Rs and that an endogenous cannabinoid is a likely candidate retrograde messenger in this preparation. They further suggest that DSI involves distinct presynaptic modifications for eIPSCs and mIPSCs, including an inhibition of action potential-evoked calcium rises.
Separating Quantum Communication and Approximate Rank

One of the best lower bound methods for the quantum communication complexity of a function H (with or without shared entanglement) is the logarithm of the approximate rank of the communication matrix of H. This measure is essentially equivalent to the approximate gamma_2 norm and generalized discrepancy, and subsumes several other lower bounds. All known lower bounds on quantum communication complexity in the general unbounded-round model can be shown via the logarithm of approximate rank, and it was an open problem to give any separation at all between quantum communication complexity and the logarithm of the approximate rank. In this work we provide the first such separation: We exhibit a total function H with quantum communication complexity almost quadratically larger than the logarithm of its approximate rank. We construct H using the communication lookup function framework of Anshu et al. (FOCS 2016) based on the cheat sheet framework of Aaronson et al. (STOC 2016). From a starting function F, this framework defines a new function H=F_G. Our main technical result is a lower bound on the quantum communication complexity of F_G in terms of the discrepancy of F, which we do via quantum information theoretic arguments. We show the upper bound on the approximate rank of F_G by relating it to the Boolean circuit size of the starting function F.
Bayesian Modeling of Dependency Trees Using Hierarchical Pitman-Yor Priors

In this paper, we describe two hierarchical Bayesian models for dependency trees. First, we show that Eisner’s classic generative dependency model [1996] can be substantially improved by (a) using a hierarchical Pitman-Yor process as a prior over the distribution over dependents of a word, and (b) sampling the model hyperparameters (section 3). These changes alone yield a signicant increase in parse accuracy over Eisner’s model. Second, we present a Bayesian dependency parsing model in which latent state variables mediate the relationships between words and their dependents. This model clusters dependencies into states using a similar approach to that employed by Bayesian topic models when clustering words into topics (section 4). The inferred states have a syntactic avor and lead to modestly improved accuracy when substituted for part-of-speech tags in the parsing model.
Reactive control of a two-body point absorber using reinforcement learning

In this article, reinforcement learning is used to obtain optimal reactive control of a two-body point absorber. In particular, the Q-learning algorithm is adopted for the maximization of the energy extraction in each sea state. The controller damping and sti ﬀ ness coe ﬃ cients are varied in steps, observing the associated reward, which corresponds to an increase in the absorbed power, or penalty, owing to large displacements. The generated power is averaged over a time horizon spanning several wave cycles due to the periodicity of ocean waves, discarding the transient e ﬀ ects at the start of each new episode. The model of a two-body point absorber is developed in order to validate the control strategy in both regular and irregular waves. In all analysed sea states, the controller learns the optimal damping and sti ﬀ ness coe ﬃ cients. Furthermore, the scheme is independent of internal models of the device response, which means that it can adapt to variations in the unit dynamics with time and does not su ﬀ er from modelling errors.
Prehistoric Settlement in Island Interiors: Evidence From California's Santa Cruz Island

ABSTRACT On California's Channel Islands, a rich body of scholarship has emerged in which the focus has been marine resources and their roles in colonization and the development of complex societies. Although this orientation has been crucial to elucidating the cultural significance of the islands, the terrestrial dimensions of island occupation have been neglected by comparison. Our research on Santa Cruz Island, the largest of the Channel Islands, is an initial step in articulating the marine and terrestrial aspects of island subsistence and settlement off the California coast. Our study is based on the compilation of radiocarbon dates from 42 sites and excavation data from 17 of these. Commonalities in artifact and faunal constituents are evident among most interior sites, although there are significant differences relating to time period. The nature of interior settlement changed dramatically through time, shifting from what are interpreted as seasonal residential bases during the Middle Holocene to the byproducts of logistical forays during the Late Holocene, with an apparent gap in occupation from 1000 BC to AD 500. In this article we evaluate patterns in these data sets in terms of multiple hypotheses that invoke climatic and cultural factors to account for interior settlement. In doing so, we highlight the shifting importance of island interiors and their terrestrial resources to coastal societies through time.
Simultaneous in vivo positron emission tomography and magnetic resonance imaging

Positron emission tomography (PET) and magnetic resonance imaging (MRI) are widely used in vivo imaging technologies with both clinical and biomedical research applications. The strengths of MRI include high-resolution, high-contrast morphologic imaging of soft tissues; the ability to image physiologic parameters such as diffusion and changes in oxygenation level resulting from neuronal stimulation; and the measurement of metabolites using chemical shift imaging. PET images the distribution of biologically targeted radiotracers with high sensitivity, but images generally lack anatomic context and are of lower spatial resolution. Integration of these technologies permits the acquisition of temporally correlated data showing the distribution of PET radiotracers and MRI contrast agents or MR-detectable metabolites, with registration to the underlying anatomy. An MRI-compatible PET scanner has been built for biomedical research applications that allows data from both modalities to be acquired simultaneously. Experiments demonstrate no effect of the MRI system on the spatial resolution of the PET system and <10% reduction in the fraction of radioactive decay events detected by the PET scanner inside the MRI. The signal-to-noise ratio and uniformity of the MR images, with the exception of one particular pulse sequence, were little affected by the presence of the PET scanner. In vivo simultaneous PET and MRI studies were performed in mice. Proof-of-principle in vivo MR spectroscopy and functional MRI experiments were also demonstrated with the combined scanner.
Black Holes in String Theory

This thesis is devoted to trying to find a microscopic quantum description of black holes. We consider black holes in string theory which is a quantum theory of gravity. We find that the ``area law'' black hole entropy for extremal and near-extremal charged black holes arises from counting microscopic configurations. We study black holes in five and four spacetime dimensions. We calculate the Hawking temperature and give a physical picture of the Hawking decay process. Hopefully, the reader will find here a moderately self contained review of D-branes and string theory applied to black hole physics.
Associations of Polymorphisms in DNA Repair Genes and MDR1 Gene with Chemotherapy Response and Survival of Non-Small Cell Lung Cancer

Objectives We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementation group 1 (ERCC1) rs11615, xeroderma pigmentosum group D (XPD/ERCC2) rs13181, X-ray repair cross complementing group 1 (XRCC1) rs25487, XRCC3 rs1799794, and breast cancer susceptibility gene 1 (BRCA1) rs1799966 from the DNA repair pathway and multiple drug resistance 1 (MDR1/ABCB1) rs1045642 with response to chemotherapy and survival of non-small cell lung cancer (NSCLC) in a Chinese population. Materials and Methods A total of 352 NSCLC patients were enrolled to evaluate the associations of the six SNPs with response to chemotherapy and overall survival. Logistic regressions were applied to test the associations of genetic polymorphisms with response to chemotherapy in 161 advanced NSCLC patients. Overall survival was analyzed in 161 advanced and 156 early stage NSCLC patients using the Kaplan-Meier method with log-rank test, respectively. Multivariate Cox proportional hazards model was performed to determine the factors independently associated with NSCLC prognosis. Results BRCA1 rs1799966 minor allele C (TC+CC vs. TT, OR = 0.402, 95%CI = 0.204−0.794, p = 0.008) and MDR1/ABCB1 rs1045642 minor allele A (GA +AA vs. GG, OR = 0.478, 95%CI = 0.244−0.934, p = 0.030) were associated with a better response to chemotherapy in advanced NSCLC patients. Survival analyses indicated that BRCA1 rs1799966 TC+CC genotypes were associated with a decreased risk of death (HR = 0.617, 95% CI = 0.402−0.948, p = 0.028) in advanced NSCLC patients, and the association was still significant after the adjustment for covariates. Multivariate Cox regression analysis showed that ERCC1 rs11615 AA genotype (P = 0.020) and smoking (p = 0.037) were associated with increased risks of death in early stage NSCLC patients after surgery. Conclusions Polymorphisms of genes in DNA repair pathway and MDR1 could contribute to chemotherapy response and survival of patients with NSCLC.
Mesothelin, a possible target for immunotherapy, is expressed in primary AML cells

Background: Mesothelin is a promising candidate for tumor‐specific therapy because of its limited expression in normal tissues and high expression in several cancers. The expression of the protein mesothelin in hematological malignancies has not yet been analyzed. SS1(dsFv)PE38 is a recombinant anti‐mesothelin immunotoxin which is undergoing clinical evaluation in patients with mesothelin‐expressing tumors.
Biomarker Analyses of Clinical Outcomes in Patients with Advanced Hepatocellular Carcinoma Treated with Sorafenib with or without Erlotinib in the SEARCH Trial

Purpose: Sorafenib is the current standard therapy for advanced hepatocellular carcinoma, but validated biomarkers predicting clinical outcomes are lacking. This study aimed to identify biomarkers predicting prognosis and/or response to sorafenib, with or without erlotinib, in hepatocellular carcinoma patients from the phase III SEARCH trial. Experimental Design: A total of 720 patients were randomized to receive oral sorafenib 400 mg twice daily plus erlotinib 150 mg once daily or placebo. Fifteen growth factors relevant to the treatment regimen and/or to hepatocellular carcinoma were measured in baseline plasma samples. Results: Baseline plasma biomarkers were measured in 494 (69%) patients (sorafenib plus erlotinib, n = 243; sorafenib plus placebo, n = 251). Treatment arm–independent analyses showed that elevated hepatocyte growth factor [HGF; HR, 1.687 (high vs. low expression); endpoint multiplicity adjusted (e-adj) P = 0.0001] and elevated plasma VEGFA (HR, 1.386; e-adj P = 0.0377) were significantly associated with poor overall survival (OS) in multivariate analyses, and low plasma KIT [HR, 0.75 (high vs. low); P = 0.0233; e-adj P = 0.2793] tended to correlate with poorer OS. High plasma VEGFC independently correlated with longer TTP (HR, 0.633; e-adj P = 0.0010) and trended toward associating with improved disease control rate (univariate: OR, 2.047; P = 0.030; e-adj P = 0.420). In 67% of evaluable patients (339/494), a multimarker signature of HGF, VEGFA, KIT, EPGN, and VEGFC correlated with improved median OS in multivariate analysis (HR, 0.150; P < 0.00001). No biomarker predicted efficacy from erlotinib. Conclusions: Baseline plasma HGF, VEGFA, KIT, and VEGFC correlated with clinical outcomes in hepatocellular carcinoma patients treated with sorafenib with or without erlotinib. These biomarkers plus EPGN constituted a multimarker signature for improved OS. Clin Cancer Res; 22(19); 4870–9. ©2016 AACR.