nils-herrmann/clean_scirepeval huggingface dataset:
New wrinkles in an old paradigm: neighborhood effects can modify the structure and specificity of Alnus-associated ectomycorrhizal fungal communities.

Host identity has been recognized as a key determinant of the structure of ectomycorrhizal (ECM) fungal communities, but the importance of neighboring ECM hosts is less well understood. To investigate the relative importance of host and neighborhood effects, we examined the ECM fungal communities associated with Alnus rhombifolia, a host of specific ECM fungi, and Betula occidentalis, a host of generalist ECM fungi. We hypothesized that the host-specific Alnus-associated ECM fungal community would not be susceptible to the influence of plant neighborhood, while the generalist Betula-associated community would. ECM fungal communities on both hosts were characterized using ITS sequences derived from conspecific and heterospecific host settings at a field site in western Idaho, USA, and from a growth chamber bioassay. In the field study, the Betula neighborhood added minor constituents to the Alnus ECM fungal community, while in the bioassay, late planting of Betula generated strong priority effects that allowed the established Alnus neighborhood to control the structure of the Betula community. Our results indicate that while host identity acts as a primary filter on the composition and diversity of ECM fungal communities, proximity to a closely related host can mediate significant changes in community structure.

Field of study: Biology, Environmental science
Local adaptation of microbial communities to heavy metal stress in polluted sediments of Lake Erie.

Microbial communities must balance the assimilation of biologically necessary metals with resistance to toxic metal concentrations. To investigate the impact of heavy metal contaminants on microbial communities, we performed two experiments measuring extracellular enzyme activities (EEA) in polluted and unpolluted sediments of Lake Erie. In the first experiment, inoculations with moderate concentrations of copper and zinc appreciably diminished EEA from uncontaminated sites, whereas EEA from contaminated sediments increased or were only negligibly affected. In the second experiment, we compared the effects of three separate metals (i.e. copper, arsenic, and cadmium) on microbial community metabolism in polluted and unpolluted locations. Although copper and arsenic elicited differential effects by inhibiting EEA only in unpolluted sediments, cadmium inhibited EEA in both polluted and unpolluted sediments. Multivariate analyses of EEA from polluted sediments revealed direct associations among hydrolytic enzymes and inverse or absent associations between hydrolases and oxidases; these associations demonstrated resilience to heavy metal stress. In contrast, addition of heavy metals to unpolluted sediments appeared to have a higher impact on the multivariate pattern of EEA associations as revealed by an increase in the number of associations, more inverse relationships, and potential enzymatic trade-offs. The results of this study suggest community-level adaptations through the development of resistance mechanisms to the types and local levels of heavy metals in the environment.

Field of study: Biology, Environmental science
Therapy for symptoms in the carcinoid syndrome.

The clinical course and results of drug treatment for manifestations of the carcinoid syndrome are reviewed in 63 patients. The five-year actuarial survival in this group of patients was 48 per cent. The only markers of a poor prognosis that could be identified at diagnosis were marked weight loss and a high (over 1000 mumol/day) 5-hydroxyindole acetic acid excretion. The relative effectiveness of well-established drugs that either block 5-hydroxytryptamine synthesis or block 5-hydroxytryptamine receptors is reported, with respect to the different manifestations of the syndrome, and compared with a small group of patients treated with long-acting somatostatin analogue. In over one-third of patients, primary tumours were not detected on initial investigation, and in none of these did symptoms referrable to the primary site become apparent later.

Field of study: Medicine
Towards an automated quality control of XAS data.

The quality of fluorescence X-ray absorption spectroscopy (XAS) data strongly depends on the identification and elimination of contributions suffering from artificial deviations. To enhance detection of deviations, XAS data are converted here to difference spectra and cumulative difference spectra. A variety of statistical criteria and procedures are examined for their application in the quality control of such data. The criterion best suited in this case is determined and a strategy for the automatic elimination of artefacts is developed: deviation-affected spectra are iteratively removed from the data pool. A threshold is defined to avoid unnecessary reduction of the experimental data pool. Exemplarily the procedure is applied for the quality control of BioXAS data.

Field of study: Physics
Diffuse large B-cell lymphoma presenting as a sacral tumor. Report of two cases.

Primary lymphomas of the sacrum are rare tumors, reported only in a few cases in the literature. The authors describe two patients with diffuse large B-cell lymphomas presenting as a sacral tumor. In the first case a 52-year-old man presented with progressive back pain, bilateral radicular pain, and saddle block anesthesia secondary to a lytic, expansile soft-tissue mass. The mass arose from the sacrum and eroded through the right S-1 to S-4 foramina and extended into the epidural space of the spinal canal. On magnetic resonance imaging, the sacral mass enhanced homogeneously with Gd. In the second case a 64-year-old man presented with left-sided radicular pain, paresthesias, and progressive weakness due to a lytic soft-tissue mass in the left sacral ala extending into the left L-5 and S-1 foramina. Metastatic workup in each patient demonstrated unremarkable findings. In both cases, an open biopsy procedure was performed after nondiagnostic examination of needle biopsy samples. Histopathological examination showed evidence consistent with diffuse large B-cell lymphoma in both patients. In the first case the disease was classified as Stage IAE, and the patient subsequently underwent four cycles of cyclophosphamide/doxorubicin/vincristine/prednisone (CHOP)- and rituximab-based chemotherapy followed by consolidation radiotherapy. In the second case the disease was also classified as Stage IAE, and the patient underwent CHOP-based chemotherapy and consolidation radiotherapy. In both cases radiography demonstrated a decrease in size of the sacral lymphomas. The authors review the clinical, radiological, and histological features of sacral lymphomas. Lymphoma should be considered in the differential diagnosis of sacral tumors.

Field of study: Medicine
GFP-tagged expression and immunohistochemical studies to determine the subcellular localization of the tubby gene family members.

The tubby gene family consists of four members, TUB, TULP1, TULP2 and TULP3, with unknown function. However, a splice junction mutation within the mouse tub gene leads to retinal and cochlear degeneration, as well as maturity onset obesity and insulin resistance. Mutations within human TULP1 have also been shown to co-segregate in several cases of autosomal recessive retinitis pigmentosa (RP) and TULP1 deficiency in mice leads to retinal degeneration. The primary amino acid sequences of the tubby family members do not predict a likely biochemical function. As a first step in defining their function, we present a detailed characterization of the cellular and subcellular localization of the human (TUB) and mouse (tub) homologous gene products. We report the isolation of TUB splice variants which have different subcellular localizations (nuclear versus cytoplasmic) and which define a nuclear localization signal. In addition, using green fluorescent protein (GFP) tags, we observe a nuclear localization for TULP1, similar to TUB splicing forms TUB 561 and TUB 506. Finally, we report tubby expression in mouse brain by in situ hybridization and by immunohistochemistry with polyclonal antibodies. Protein was found in both the hypothalamic satiety centers and in a variety of other CNS structures including the cortex, cerebellum, olfactory bulb and hippocampus. Both nuclear and cytoplasmic signals were detected with a series of independently generated polyclonal antibodies, consistent with the presence of multiple alternatively spliced isoforms within the CNS.

Field of study: Biology
Structural changes in electrochemically cycled LiMn0.7Fe0.3PO4

Li(1−x)Mn0.7Fe0.3PO4 (0.00 ≤ x ≤ 1.0) samples, obtained by electrochemical cycling, were investigated by powder X-ray diffraction (XRD) and Fourier-transform infrared spectroscopy (FTIR). The purpose of this work is to map phase transition information for samples at quasi equilibrium i.e. after a long relaxation time. The required high accuracy solid Li+ content was determined by atomic emission using the standard addition method. From XRD analysis of the charging cycle samples, the phase diagram was shown to exhibit a solid solution (0 ≤ x ≤ 0.42), followed by a two phases system exhibiting both olivine and heterosite structures (0.42

Field of study: Materials science
De Causis Linguae Latinae (Lyon, 1540) / Des causes de la langue latine. Jules-César Scaliger. Ed. and trans. Pierre Lardet, Geneviève Clerico, and Bernard Colombat. 2 vols. Travaux d'Humanisme et Renaissance 594. Geneva: Droz, 2018. 2,222 pp. $222.

pretive work—no less responsive to Erasmus’s texts, but less anxious for them—can proceed. This is also of course the moment to reopen some of the fundamental questions of authorial intent and method that editors and annotators of the Paraphrases have repeatedly had to address along the way. One of them concerns the intended readership of these singularly Erasmian texts. Introducing a set of conference proceedings some years ago, I called them “virtual scripts for preaching” (cited here at 5n26). “The Paraphrases are aimed at a readership of the more, or less educated clergy,” Bloemendal infers (3). But it is not clear from the passages adduced that only clergy are in view, and the wider franchise of theologizing modeled—so disconcertingly to the likes of Bede—by the Ratio Verae Theologiae (1518/19) suggests otherwise. On balance, Bateman’s choice in favor of “students or accomplished theologians, clergy or laity” (ASD VII-6, 1) still looks safer. A second critical question concerns the use made by Erasmus in this case of “the compilation works Glossa ordinaria (edited as Biblia cum glossa, including the commentary by Nicolaus Lyranus), Thomas Aquina[s]’s Catena aurea and Beda’s [i.e., Bede’s] In Lucam expositio” (34), Bede’s commentary being also essentially a compilation. Differing from Phillips, Bloemendal argues, first, that Erasmus as a rule only checked “mainstream exegesis” after he had made a draft of his paraphrase of a passage and, second, that the works that he used for such checking were “primarily” the compilation works listed above, rather than texts of the church fathers such as he elsewhere (e.g., in the Ratio Verae Theologiae) urged his readers to consult at first hand. While Erasmus’s recourse to such works has long been recognized, Bloemendal’s assessment of their role entails a significant revision of the working model for the composition of the Paraphrases formerly proposed by Bateman on the basis of a suggestion made by Irena Backus (see ASD VII-6, 13, cited ASD VII-2, 26–27). The means of verifying that assessment are now—or, in the case of the rest of this ordo, soon will be—before us.

Field of study: History
Computational toxicology: Physiologically based pharmacokinetic models (PBPK) for lifetime exposure and bioaccumulation of polybrominated diphenyl ethers (PBDEs) in marine mammals.

Due to migration of harbour porpoises towards more polluted areas like the North Sea and their sensitivity towards pollution, there is a need for proper conservation measures for this species. As a consequence, knowledge about the pollutant's kinetics is required. The present study is the first to investigate the kinetics of PBDEs in marine mammals using PBPK modeling as a non-destructive tool for describing the chemical's kinetics in a protected animal species. The models were developed and parameterized using data from the literature and Black Sea harbour porpoises through computer optimization. The predictability of these models in time was assessed by reverse dosimetry modeling using data from North Sea porpoises (1990-2008). From these predictions, PBDE 99 levels were found to decrease the fastest, followed by PBDE 153, 47 and 100. Results show that the PBPK models can be applied for harbour porpoises from different regions and also simulate time trends.

Field of study: Environmental science
Verfärbung und Lumineszenz. VI

ZusammenfassungIm folgenden wird wieder eine Übersicht über die vom Verfasser und seinen Mitarbeitern (Dr. H.Adler, Dr.Hanne Ellis-Lauda, Dr.Ingrid Kveta, F.Steg-müller und Dr. K.Treitl) ausgeführten Arbeiten über Verfärbung und Lumineszenz gegeben, mit einigen ergänzenden Bemerkungen, wobei diesmal auch Lumineszenzen in Betracht gezogen werden, die nichts mit Becquerel-Strahlen zu tun haben.

Field of study: Physics
Impact of oxygen plasma beams on spacecraft materials

The effect oxygen plasma with energies of 20–30 eV has on a number of materials is studied by simulating their exposure on orbital spacecraft during long duration flights in the ionosphere. The effects of changes in the thermal and optical properties of ECOM-2 black thermoregulation coating and the destruction of the aramid fibers in PRUSMl shielding braid and Scotch 431 protective polyether layer tape that degrade their material properties are described.

Field of study: Physics
Dynamics of relativistic SCRs and registration of multiple neutrons during the event of December 13, 2006

The dynamics of relativistic SCRs during the event of December 13, 2006, the characteristics of which were obtained from the neutron monitor data by solving the inverse problem, has been studied. A strongly collimated flux of relativistic protons, which caused an impulse-like increase at several European stations, was registered during the event initial phase. The delayed component had a softer spectrum and a large isotropic component. The Barentsburg neutron monitor registered a significant increase in neutrons with multiplicities of 2–4 during the event of December 13, 2006.

Field of study: Physics
DIDS Reduces Ischemia/Reperfusion-Induced Myocardial Injury in Rats

Anion channels such as chloride channel are known to participate in the regulation of a wide variety of cellular processes including development, differentiation, proliferation, apoptosis and regeneration. This study was designed to examine the effect of the non-selective anion channel blocker 4,4'-Diisothiocyanostilbene-2, 2'-disulfonic acid (DIDS) on cardiac function and apoptosis using a rat model of ischemia/reperfusion (I/R).  Fifty male SD rats were randomly divided into the following groups including sham, I/R and I/R+DIDS (7, 14 or 28 mg/kg). In DIDS group, rats received DIDS treatment (4 ml/kg/hr) at the beginning of reperfusion for 2 hrs using a programmed micro-pump. Cardiac function was evaluated including left ventricular systolic pressure (LVSP), left ventricular end diastolic pressure (LVEDP) as well as positive and negative maximal derivatives of left ventricular pressure (± dP/dtmax). Myocardial infarct size was detected using the double staining with 2, 3, 5-triphenyl-2H-tetra-zolium chloride (TTC) and Evan's blue dye. DNA ladder, TUNEL assay, Bax and Bcl-2 protein levels were evaluated. Levels of ROS and Akt phosphorylation were detected.  I/R injury compromised cardiac function as manifested by reduced LVSP and ± dP/dtmax as well as pronounced apoptosis. I/R-induced cardiac anomalies were markedly ameliorated by DIDS. DIDS retarded I/R-induced myocardial infarct and apoptosis. In addition, DIDS ameliorated I/R-induced ROS production and Akt dephosphorylation in the heart.  Taken together, our data revealed that DIDS may protect cardiomyocytes against I/R injury as evidenced by improved cardiac function, Bcl-2, Akt phosphorylation, and reduced myocardial apoptosis, Bax expression, ROS production and myocardial infarct size.

Field of study: Biology, Chemistry
Vaccination of neonatal calves with Mycobacterium bovis BCG induces protection against intranasal challenge with virulent M. bovis

Vaccination of neonates with Mycobacterium bovis bacillus Calmette–Guérin (BCG) may be a strategy that overcomes reduced vaccine efficacy associated with exposure to environmental mycobacteria in humans and cattle. Preliminary comparisons indicated that 2‐week‐old calves produced an immune response to vaccination at least as intense as that observed in adults. Subsequently, five gnotobiotic hysterotomy derived calves aged 1 day were inoculated with BCG and 3 months later were challenged intranasally with virulent M. bovis. The number of tissues with lesions and the pathological extent of these lesions was reduced significantly in vaccinates. Furthermore, lesions were evident in the lung or associated chest lymph nodes of four of five controls but none of five vaccinates. BCG vaccination reduced significantly the level of bacterial colonization. However, lesions in the head associated lymph nodes were observed in three of five BCG‐vaccinated cattle. Levels of interferon gamma (IFN‐γ) detected by enzyme‐linked immunosorbent assay (ELISA) or enzyme‐linked immunospot (ELISPOT) in individual vaccinated animals at challenge did not correlate with subsequent resistance and in general immune responses post‐challenge were lower in vaccinated calves. Low IL‐10 responses were evident but IL‐4 was not detected. Responses to ESAT‐6 and/or CFP‐10 were evident in four of four control calves that had lesions. Two of the BCG vaccinates with lesions did not produce a response to ESAT‐6 and CFP‐10, indicating that these antigens did not distinguish vaccinated immune animals from vaccinated animals with lesions. Overall, vaccination of neonatal calves with BCG induced significant protection against disease and has potential as a strategy for the reduction of the incidence of bovine tuberculosis.

Field of study: Biology, Medicine
The impact of natural product chemistry on medicine

When invited to present this lecture I was assured that this subject would provide a unique opportunity for perspectives. Not only was this correct, but this subject has been a unique trial for decisions on which products to exclude and include; I have excluded antibiotics, but pay tribute to their vast importance in medicine. As a policy, contributions directly or indirectly from the chemistry of natural products are interpreted broadly, and I decided to minimize historical aspects and to maximize recent and current aspects of chemistry and medicine. Because most of us are interested in the future, I have included trends and medical objectives of great significance for new

Field of study: Chemistry
RESEARCH ON FORCE CONTROL THEORY OF ADAPTIVE BEAM STING STRUCTURE

An adaptive beam string structure was a form of an intelligent structure, which can control the working status by adjusting the prestress of the structure according to the changes of external loads. Firstly, the working mechanism of the structure was analyzed. Next, the equations of structural force status were established.And then the force control problem of slack of the lower chord cable caused by the negative air pressure was analyzed, and the corresponding control model was built. Furthermore, the force control problem of the inhomogeneous internal force of an upper chord beam caused by moving loads was analyzed, while the load space was divided into controllable regions with a time lag or not according to the magnitude and the moving velocity of moving loads. The control model of each controllable region was built respectively for optimising structural force status. Finally, a numerical example was conducted to verify the working performance of the structure. Numerical results demonstrate that: in the comparison with a normal beam string structure, an adaptive beam string structure can reduce the peak force and initial prestress level as well as improve bearing capacity by adaptive control.

Field of study: Engineering
Optimal Weighting of Multi-View Data with Low Dimensional Hidden States

In Natural Language Processing (NLP) tasks, data often has the following two properties: First, data can be chopped into multi-views which has been successfully used for dimension reduction purposes. For example, in topic classification, every paper can be chopped into the title, the main text and the references. However, it is common that some of the views are less noisier than other views for supervised learning problems. Second, unlabeled data are easy to obtain while labeled data are relatively rare. For example, articles occurred on New York Times in recent 10 years are easy to grab but having them classified as 'Politics', 'Finance' or 'Sports' need human labor. Hence less noisy features are preferred before running supervised learning methods. In this paper we propose an unsupervised algorithm which optimally weights features from different views when these views are generated from a low dimensional hidden state, which occurs in widely used models like Mixture Gaussian Model, Hidden Markov Model (HMM) and Latent Dirichlet Allocation (LDA).

Field of study: Computer science
ENERGY REQUIREMENTS FOR CONVENTIONAL TILLAGE FOLLOWING DIFFERENT CROP ROTATIONS

Energy savings can be made by improving tractor and implement performance during tillage. We studied the 
relationship between cropping history and energy requirements for moldboard plowing and seedbed preparation 
(two passes with a field cultivator) on a loam soil under nine previous management practices, ranging from 6-year 
bromegrass (Bromus inermis Leyss.) to 6-year conventional-till corn (Zea mays L.). Soil bulk density ( nb) and volumetric 
water content ( e) were measured before tillage. Draft, specific draft, ground speed, wheel slip, fuel consumption and plow 
depth were monitored during primary and secondary tillage using a 97 kW instrumented tractor. The nb, eand all of the 
primary tillage performance variables were significantly influenced by cropping history. Plow depth increased with 
decreasing nb (r = –0.41*). Draft (r = 0.44**), specific draft (r = 0.40*), wheel slip (r = 0.40*), and fuel consumption (r = 
0.35*) increased with increasing e, while ground speed decreased (r = –0.39*). The effects of previous management on 
tillage energy became less pronounced as number of secondary tillage operations increased. Soil fragmentation (Df) was 
measured after tillage, and was similar for all of the treatments despite different amounts of energy expended. 
Conventional tillage operations following long-term forages increase the energy required to produce a corn crop relative 
to continuous conventional-till corn.

Field of study: Agricultural and Food sciences
ABioTrans: A Biostatistical Tool for Transcriptomics Analysis

Here we report a bio-statistical/informatics tool, ABioTrans, developed in R for gene expression analysis. The tool allows the user to directly read RNA-Seq data files deposited in the Gene Expression Omnibus or GEO database. Operated using any web browser application, ABioTrans provides easy options for multiple statistical distribution fitting, Pearson and Spearman rank correlations, PCA, k-means and hierarchical clustering, differential expression (DE) analysis, Shannon entropy and noise (square of coefficient of variation) analyses, as well as Gene ontology classifications.

Field of study: Biology