nils-herrmann/clean_scirepeval huggingface dataset:
Exome capture and massively parallel sequencing identifies a novel HPSE2 mutation in a Saudi Arabian child with Ochoa (urofacial) syndrome.

We describe a child of Middle Eastern descent by first-cousin coupling with idiopathic neurogenic bladder and high-grade vesicoureteral reflux at 1 year of age, whose characteristic facial grimace led to the diagnosis of Ochoa (urofacial) syndrome at age 5 years. We used homozygosity mapping, exome capture and paired-end sequencing to identify the disease causing mutation in the proband. We reviewed the literature with respect to the urologic manifestations of Ochoa syndrome. A large region of marker homozygosity was observed at 10q24, consistent with known autosomal recessive inheritance, family consanguinity and previous genetic mapping in other families with Ochoa syndrome. A homozygous mutation was identified in the proband in HPSE2: c.1374_1378delTGTGC, a deletion of 5 nucleotides in exon 10 that is predicted to lead to a frameshift followed by replacement of 132 C-terminal amino acids with 153 novel amino acids (p.Ala458Alafsdel132ins153). This mutation is novel relative to very recently published mutations in HPSE2 in other families. Early intervention and recognition of Ochoa syndrome with control of risk factors and close surveillance will decrease complications and renal failure.

Field of study: Medicine
Comparison of two crystal structures of TGF-beta2: the accuracy of refined protein structures.

Transforming growth factor-beta is a multifunctional cell-growth regulator and is a member of the TGF-beta superfamily of cytokines. Each monomer is 112 amino acids long and the mature active form is a 25 kDa homodimer. Recently, the crystal structure of TGF-beta2 has been determined independently in two laboratories [Daopin, Piez, Ogawa & Davies (1992). Science, 257, 369-373; Schlunegger & Grütter (1992). Nature (London), 358, 430-434] and subsequently refined to higher resolutions [Daopin, Li & Davies (1993). Proteins Struct.  (1993). ]. A detailed structural comparison shows that the two structures are nearly identical with the differences mostly located on the mobile regions of the molecule. The r.m.s. differences between the two structures are 0.10 A for 104 pairs of C(alpha) atoms, 0.15 A for 434 pairs of main-chain atoms, 0.33 A for 860 out of 890 pairs of protein atoms and a correlation of 90% between the temperature B factors of all protein atoms. Based on a comparison of the water molecules, a B value of 60.0 A(2) is recommended as the cut off for modeling new waters. The structural identity is striking because in one case the material was expressed in vivo in CHO cells whereas in the other case it was expressed in E. coli and had to be refolded in vitro. The overall coordinate errors are estimated to be 0.21 A from the Luzzati plot, 0.18 A from the sigma(A) plot, 0.24 A with Cruickshank's equations and 0.25 A using the empirical method of Perry & Stroud. These estimates are comparable to the r.m.s. structure superposition. The r.m.s. differences correlate very well with the crystallographic B values and the relation is best described with the Cruickshank formula. In addition to the estimation of an overall error, a new application of the Cruickshank formula is presented here to estimate the local errors.

Field of study: Chemistry
The First Year Colloquium: Creating a Safe Space for Students to Flourish

College is one of the most formative times in an individual’s life. Its intense living-learning environment can promote students’ extreme self-confidence and positive development, or alternatively, can result in low levels of well-being. The first year in college is an opportunity for faculty and staff to engage with students to help them build learning skills, a sense of responsibility, and ownership of their college experiences. The aim of this study was to examine the impacts of a first year colloquium on student well-being. In the fall of 2015, 91 entering first year students at Georgetown University in Washington, DC, participated in a mixed method study using written reflection responses and in a pre/post survey using Keyes (2009) Mental Health Continuum-Short Form (MHC-SF). Gains were seen in psychological well-being with an increase in flourishing as compared to early semester moderate flourishing. Students reported that having one course that provided a safe space for them in their first semester, and that addressed well-being in college, was critical for them to succeed and thrive in their first year.

Field of study: Education
Über das wellenmechanische Zweizentrenproblem

ZusammenfassungDie vorliegende Arbeit enthält eine Übersicht Über verschiedene Typen von Lösungen des wellenmechanischen Zweizentrenproblems, nebst einer neuen Berechnung vom Grundzustand des WasserstoffmolekÜlions mit Hilfe einer explizit gegebenen Wellenfunktion.

Field of study: Physics
Adaptive step-size algorithms for blind interference suppression in DS/CDMA systems

This paper develops adaptive step-size blind LMS algorithms and adaptive forgetting factor blind RLS algorithms for code-aided suppression of multiple access interference (MAI) and narrowband interference (NBI) in DS/CDMA systems. These algorithms optimally adapt both the step size (forgetting factor) and the weight vector of the blind linear multiuser detector using the received measurements. Simulations are provided to compare the proposed algorithms with previously studied blind RLS and blind LMS algorithms. They show that the adaptive step-size blind LMS algorithm and adaptive forgetting factor blind RLS algorithm field significant improvements over the standard blind LMS algorithm and blind RLS algorithm in dynamic environments where the number of interferers are time-varying.

Field of study: Engineering
Werner Syndrome-specific induced pluripotent stem cells: recovery of telomere function by reprogramming

Werner syndrome (WS) is a rare human autosomal recessive premature aging disorder characterized by early onset of aging-associated diseases, chromosomal instability, and cancer predisposition. The function of the DNA helicase encoded by WRN, the gene responsible for WS, has been studied extensively. WRN helicase is involved in the maintenance of chromosome integrity through DNA replication, repair, and recombination by interacting with a variety of proteins associated with DNA repair and telomere maintenance. The accelerated aging associated with WS is reportedly caused by telomere dysfunction, and the underlying mechanism of the disease is yet to be elucidated. Although it was reported that the life expectancy for patients with WS has improved over the last two decades, definitive therapy for these patients has not seen much development. Severe symptoms of the disease, such as leg ulcers, cause a significant decline in the quality of life in patients with WS. Therefore, the establishment of new therapeutic strategies for the disease is of utmost importance. Induced pluripotent stem cells (iPSCs) can be established by the introduction of several pluripotency genes, including Oct3/4, Sox2, Klf4, and c-myc into differentiated cells. iPSCs have the potential to differentiate into a variety of cell types that constitute the human body, and possess infinite proliferative capacity. Recent studies have reported the generation of iPSCs from the cells of patients with WS, and they have concluded that reprogramming represses premature senescence phenotypes in these cells. In this review, we summarize the findings of WS patient-specific iPSCs (WS iPSCs) and focus on the roles of telomere and telomerase in the maintenance of these cells. Finally, we discuss the potential use of WS iPSCs for clinical applications.

Field of study: Biology
Effect of space charge and nonuniform temperature on a solid state galvanic cell

The complete set of differential equations of nonequilibrium thermodynamics has been solved for a solid state galvanic cell consisting of single electrolyte sandwiched between electrodes. Electroneutrality is not assumed anywhere, and it is therefore possible to assess the effects of nonzero space charge in the electrolyte near the electrodes. A special transformation of concentration variables into a neutral part and a charge part facilitates both the analytical and the numerical solution of the mathematical problem. Formulas are obtained for the electric field, the ionic concentration, the space charge, the cell potential, and the efficiency of the cell at steady state. Inclusion of appropriate temperature gradient terms in all equations permits evaluation of the effects of nonuniform temperature on all cell properties including efficiency. For specificity, numerical results are obtained for the particular galvanic cell consisting of cerium oxide doped with calcium oxide as the electrolyte contained between oxygen electodes. Efficiency is enhanced — more current is produced with less ohmic loss — if the product Q ∗ (ΔT) is negative, with Q ∗ the heat of transport of the electrolyte and ΔT the temperature difference between the cathode and the anode.

Field of study: Materials science
Diatom‐driven recolonization of microbial mat‐dominated siliciclastic tidal flat sediments

Modern microbial mats and biofilms play a paramount role in sediment biostabilization. When sporadic storms affect tidal flats of Bahía Blanca Estuary, the underlying siliciclastic sediment is exposed by physical disruption of the mat, and in a few weeks' lapse, a microbial community re‐establishes. With the objective of studying colonization patterns and the ecological succession of microorganisms at the scale of these erosional structures, these were experimentally made and their biological recolonization followed for 8 weeks, with replication in winter and spring. Motile pennate diatoms led the initial colonization following two distinct patterns: a dominance by Cylindrotheca closterium in winter and by naviculoid and nitzschioid diatoms in spring. During the first 7 days, cell numbers increased 2‐ to 17‐fold. Cell densities further increased exhibiting sigmoidal community growth, reaching 2.9‐8.9 × 106 cells cm−3 maxima around day 30; centric diatoms maintained low densities throughout. In 56 days after removal of the original mat, filamentous cyanobacteria that dominate mature mats did not establish a significant biomass, leading to the rejection of the hypothesis that cyanobacteria would drive the colonization. The observed dominance of pennate diatoms is attributed to extrinsic factors determined by tidal flooding, and intrinsic ones, e.g. motility, nutrient affinity and high growth rate.

Field of study: Biology, Environmental science
Effects of Condenser Drum Covering at Cotton Gins on Card Room Dust and Quality of Yarn Produced by Open-End Spinning

STUDIES were conducted to determine whether the wire mesh used on condenser drums at cotton gins in-creased the card room dust levels and had any adverse ef-fects on the quality of yarn produced by open end spin-ning. The investigation included five combinations of condenser drum coverings at two seed-cotton cleaning levels. Data collected indicate the card room dust levels were affected by the condenser drum coverings at the max-imum level of seed-cotton cleaning, but not at the minimum level. Data regarding the quality of yarn pro-duced by the open end spinning process indicated that none of the measured yarn-quality variables were adversely affected by condenser drum coverings when processing seed-cotton at the maximum seed-cotton cleaning level. Only the skein-break factor and the single-strand yarn strength were affected at the minimum seed-cotton cleaning level.

Field of study: Agricultural and Food sciences
Time Domain Finite Element Analysis of Dynamic Systems

In this study, dynamic analyses of systems are conducted using the time domain finite element analysis when initial and final conditions are specified. Dynamics of systems can be analyzed using the time-marching procedure based on Hamilton's weak principle. A new method is developed to describe the motion of a system and is extended to accommodate the initial displacement as a state variable. System matrices are constructed to evaluate time histories of the system from initial time to a specified time without the information on the velocity and momentum at each time step. Galerkin's weak principle is used to construct element matrices in the time domain and assemble the whole matrices. The Neumann boundary condition is modified to reflect the effect of initial displacement and velocity that are inherent to dynamic problems through the momentum conservation of the system. The matrices obtained thereafter conserve the symmetricity and enable us to reduce the model order by the systematic approach. Spatial propagation equation is built up, and two-point boundary conditions are used to estimate the unknown initial conditions at one end of the beam. Modal domain analysis is introduced to reduce the size of matrices. It can be seen that the matrices constructed using the time domain finite element analysis are applicable to the model reduction that is analogous to the space-domain model reduction methodology. Several numerical examples show that a consequence of the suggested method can be applied to describe the motion of various dynamic systems successfully and to validate the effect of the model reduction in the time domain.

Field of study: Physics
Performance and Quench Characteristics of a Pancake Coil Wound With the 2G YBCO Roebel Cable

The YBCO Roebel cable is a promising option for the high-energy accelerator magnets and tokamak devices with high-current carrying capability and compactness. Referring to the complex current sharing and normal zone propagation, it is difficult to apply the traditional superconductor quench measurement methodology to such a long Roebel cable (2 m) in an adiabatic condition. An alternative method for the quench measurement is to make a Roebel pancake coil cowound with ribbon fiberglass. This paper starts reporting the methodology to wind the coil with impregnation process and the wire installment for the quench measurement. Some initial performance measurements and a first trial of the quench measurement were processed in LN2 at 77 K to show the robust performance of this Roebel cable at all the current contacts while maintaining the cable effectively adiabatic or similar to real magnets.

Field of study: Physics
Bats benefit from beavers: a facilitative link between aquatic and terrestrial food webs

Bat populations are declining in many areas, partly because up to two-thirds of their wetland habitats have been lost. One natural agent creating wetlands is the beaver, which is recolonizing its former range. Beaver flowages are known for their high production of aquatic invertebrates. We tested the hypothesis that the high numbers of insects emerging from beaver flowages influences their use by foraging bats. We compared bat use and bat numbers above flowages of introduced Canadian beavers Castor canadensis and in nearby control ponds where beavers were absent. The two bat species detected, Eptesicus nilssoni and Myotis daubentoni, used beaver flowages more than non-beaver ponds. This is especially the case for Eptesicus nilssoni. Bats also seemed to forage in larger groups while above beaver ponds compared to the control ponds. Beaver flowages appeared to improve bat habitats. A plausible reason for this could be the high number of insects emerging from beaver ponds. Favouring the beaver in habitat management is a tool for creating suitable conditions for many other species, such as bats. In areas not suited for the beaver, insect production can be achieved by imitating the beaver with man-made impoundments. This is especially important in areas which have lost most of their wetlands.

Field of study: Environmental science
Strata containing the Jurassic flora of Oregon

Two fossil floras have been reported from the Mesozoic rocks of California and Oregon, the one Cretaceous and the other Jurassic. With the former the fauna is Cretaceous, but with the latter the fauna has been regarded as a matter of doubt. It is the purpose of this paper to remove the doubt by showing that in part of Oregon and California the Jurassic flora, as illustrated in the accompanying diagram, is in the “Myrtle” and Knoxville beds, while elsewhere it extends down to the horizon of the Mariposa, and the general conclusion is reached that for the Pacific coast the line between the Cretaceous and the Jurassic is the great unconformity at the base of the Knoxville.  The discovery of fossil plants by Aurelius Todd in Douglas county, Oregon, more than thirty years ago has led finally, through the collections of Will Q. . . .

Field of study: Geology
Simulation and Analysis on Performance of the Multi-path Load Balance

If a large file transmitted in a condition of network congestion, It would caused very long file download response time with all packets are transferred from the source to the destination via a single path. Open shortest path first algorithms with multi-path load balancing are designed on the computer network simulation platform, some network performance parameters such as file download response time and link throughput can be obtained. The results shows that network resources can be optimized by using multi-path load balancing protocol in the network level. If User Datagram Protocol (UDP) was used as transport protocol, we can get even fewer file download response time and thereby network performance was improved.

Field of study: Computer science
Selection using “play-the-winner” sampling for non-negative observations

The problem of choosing the best of k populations when observations are non-negative and small observations are preferred is considered using a truncated play-the-winner sampling scheme. Upper bounds on the expected sample sizes are derived. The procedure is compared with a fixed sample size procedure on the basis of expected sample size and of risk. It is noted that the probability of correct selection (P.C.S.) is the same for the two procedures so that existing tables may be used.

Field of study: Mathematics
SCALE ECONOMIES IN THE ADMINISTRATION OF LOCAL GOVERNMENT

: Part of the argument put forward in support of amalgamating local government authorities is that large councils have advantages of economies of scale. This article quantifies scale economies by a range of expenditure functions. It shows that amalgamation benefits may be as readily achieved through combining functions as in changing geographic boundaries. Furthermore, the study provides clear evidence that larger councils not only offer more services to ratepayers than smaller councils, but receive less support per capita than small councils from state and commonwealth government sources. This latter conclusion has important implications for those charged with the task of administering the scarce funds available through intergovernment financial arrangements.

Field of study: Political science
The Effect of Commitment on Information Utilization in the Attribution Process

The hypothesis that increased behavioral commitment causes increased utilization of information about a communicator was tested. Commitment to a position (public or private speech), communicator's situational description (mand or tact), and communication discrepancy (consonant or discrepant) were varied factorially. The situational description of the communicator significantly influenced attributions of causality with high but not with low commitment.

Field of study: Psychology
Multiscale, Multigranular Statistical Image Segmentation

We consider a problem in image segmentation in which the goal is to determine and label a relatively small number of homogeneous subregions in an image scene, based on multivariate, pixelwise measurements. Motivated by current challenges in the field of remote sensing land cover characterization, we introduce a framework that allows for adaptive choice of both the spatial resolution of subregions and the categorical granularity of labels. Our framework is based on a class of models that we call mixlets, a blending of recursive dyadic partitions and finite mixture models. The first component of these models allows for the sparse representation of a spatial structure at multiple resolutions. The second component provides a natural mechanism for capturing the varying degrees of mixing of pure categories that accompany the use of different resolutions and for relating these to a user-specified hierarchy of labels at multiple granularities in a straightforward manner. A segmentation is produced in our framework by selecting an optimal mixlet model, through complexity-penalized maximum likelihood, and summarizing the information in that model with respect to the categorical hierarchy. Both theoretical and empirical evaluations of the proposed framework are presented.

Field of study: Mathematics
Observation of surface precipitation of arsenate on ferrihydrite.

X-ray diffraction and Raman spectroscopy were used in this study to characterize arsenate phases in the arsenate-ferrihydrite sorption system. Evidence has been obtained for surface precipitation of ferric arsenate on synthetic ferrihydrite at acidic pH (3-5) underthe following experimental conditions: sorption density of As/Fe approximately 0.125-0.49 and arsenic equilibrium concentration of <0.02-440 mg/L. Surface precipitation occurred under apparently undersaturated (in the bulk solution phase) conditions, and probably involved initial uptake of arsenate by surface complexation followed by transition to ferric arsenate formation on the surface as indicated by XRD analysis. At basic pH (i.e., pH 8), however, no ferric arsenate was observed in arsenate-ferrihydrite samples at a sorption density of As/Fe approximately 0.125-0.30 and an arsenic equilibrium concentration of 2.0-1100 mg/ L. At pH 8, arsenate is sorbed on ferrihydrite predominantly via surface adsorption, and the XRD patterns resemble basically that of ferrihydrite.

Field of study: Environmental science
Preparation and the immunogenicity of the conjugate made from group A capsular polysaccharide and group B outer membrane protein complex of Neisseria meningitidis

To prepare the conjugate of ACPS and outer membrane protein complexes (OMPC) of Neisseria meningitidis ( Nm ) and to study its immunogenicity was OMPC purified from the strain 3407 or 542852.  OMPC was purified on Sephacryl S 300 HR after the cultural supernatants were precipitated by 70% ammonium sulfate. ACPS was conjugated to OMPC of serogroup B (BOMPC) by carbodiimide mediated condensation. Mice were respectively immunized by the conjugates, unconjugated ACPS, BOMPC and simple mixture of ACPS and BOMPC in the same procedure, then the immunogenicity of the conjugates was determined by ELISA, bactericidal test and Western blotting.  The immunogenicity of the conjugates was enhanced by 21 to 320 times as large as the unconjugated ACPS or the simple mixture of ACPS and BOMPC. The effect of conjugation of ACPS to the strain 3407 OMPC was better than that to the strain 542852 OMPC. Antisera evoked by BOMPC ACPS conjugates not only possessed a stronger bactericidal activity to the serogroup A strains (29019) and the serogroup B strains (3407, 542852, 29021) but also showed broadly cross reactions to other eight serogroup B strains of different bacterial types. It was primarily found by Western blotting analysis that the sera elicited by the above conjugates obviously reacted with M ?r?42000, 39000 and 26000 proteins in OMPC. Among the reactive bands, the 42kD protein was classⅠOMP.  The above conjugates not only possessed strong immunogenicity of Nm serogroup A and serogroup B but also enhanced the immunogenicity of ACPS to mice.

Field of study: Biology