nils-herrmann/clean_scirepeval huggingface dataset:
Computer-Based Exercises To Supplement the Teaching of Stereochemical Aspects of Drug Action.

The development of innovative strategies to teach key stereochemical concepts has been an ongoing, evolutionary process at our University. Initially, the ALCHEMY molecular modeling program was used to give demonstrations within the lecture hall setting. While successful, these demonstrations did not allow student active learning. Thus, a more interactive approach was sought. To this end, a tutorial manual composed of five self-paced, computer exercises was developed. These exercises also utilize the ALCHEMY molecular modeling program and have been used for the past two years. Students work in small groups and complete these exercises in Duquesne University’s School of Pharmacy Computer Laboratory under the supervision of a teaching assistant or the course instructor. The success of this method was assessed using student evaluations and examination questions. Overall, this teaching method has been well received and appears to increase the students’ understanding of stereochemical concepts as they relate to drug action.

Field of study: Education, Medicine
Scanning Hartmann inspection apparatus

A scanning Hartmann inspection apparatus has been developed on the basis of the traditional Hartmann test principle.It can inspect large-aperture focusing lenses up to 300 mm in diameter within the full aperture.The apparatus consists of a large-aperture collimator,a scanning Hartmann screen,a focusing lens to be tested,a CCD camera and a computer.The longitudinal aberration and the encircled energy of the aspheric collimating lens of the Fizeau plane interferometer with the effective aperture of 154 mm are measured,and it is tested by a WYKO interferometer as well.The results obtained from the two above mentioned methods agree well,which proves that the scanning Hartmann inspection apparatus is reliable.

Field of study: Physics
A Unifying Bayesian View of Continual Learning

Some machine learning applications require continual learning - where data comes in a sequence of datasets, each is used for training and then permanently discarded. From a Bayesian perspective, continual learning seems straightforward: Given the model posterior one would simply use this as the prior for the next task. However, exact posterior evaluation is intractable with many models, especially with Bayesian neural networks (BNNs). Instead, posterior approximations are often sought. Unfortunately, when posterior approximations are used, prior-focused approaches do not succeed in evaluations designed to capture properties of realistic continual learning use cases. As an alternative to prior-focused methods, we introduce a new approximate Bayesian derivation of the continual learning loss. Our loss does not rely on the posterior from earlier tasks, and instead adapts the model itself by changing the likelihood term. We call these approaches likelihood-focused. We then combine prior- and likelihood-focused methods into one objective, tying the two views together under a single unifying framework of approximate Bayesian continual learning.

Field of study: Computer science
Dietary response of early Pleistocene ungulate communities to the climate oscillations of the Gelasian/Calabrian transition in Central Italy

Climatic oscillations at the Gelasian/Calabrian transition modified terrestrial palaeoenvironmental settings in the European region. A gradual drop in global temperatures beginning about 2.7 Ma led to drier conditions and to a reduction in, and subsequent disappearance of, sub-tropical vegetation in the central Mediterranean area by ca 1.2 Ma. Large ungulates are sensitive to vegetation changes and faced with harsher environmental settings may shift their feeding strategies to exploit available food resources in different ecosystems. In fossil assemblages such dietary adaptations are reflected by tooth morphology (a phylogenetic signal) and tooth wear degree (a direct signal of the species' diet). In this paper, we investigate how large herbivores responded to palaeoenvironmental changes that occurred at the passage between the Gelasian and Calabrian ages in the Italian Peninsula, analysing the dental wear patterns and hypsodonty of the early Pleistocene fossil ungulates assemblage of Olivola (Aulla, Central Italy). We found that while ungulate feeding behaviours during the Gelasian spanned from browsers to grazers, in the locality of Olivola this group of herbivores display a narrower range of diet types with many taxa adopting a mixed feeding behaviour. Cervids in particular, whose fossils are often associated only with wooded environments, as a response to the reduction of covered sub-tropical vegetation, shifted from a strict browsing diet in mostly closed habitats to a more abrasive one taking advantage of the spread of open landscapes. We also provide new data on the feeding behaviour of the rare fossil caprines, Procamptoceras and Gallogoral meneghinii, suggesting a grass-rich mixed diet for the former and a certain degree of dietary plasticity for the latter. Our research thus contributes to the better understanding of how ungulates adapted in the past to exploit different resource types during pivotal climatic changes and how environments changed in Central Italy on the onset of colder and more arid conditions.

Field of study: Environmental science, Geography
Rotational Damping And Compound Formation In Warm Rotating Nuclei

The rotational damping width Γrot and the compound damping width Γcomp are two fundamental quantities that characterize rapidly rotating compound nuclei having finite thermal excitation energy. A two‐component structure in the strength function of consecutive E2 transitions reflects the two widths, and it causes characteristic features in the double and triple gamma‐ray spectra. We discuss a new method to extract experimentally values of Γrot and Γcomp. The first preliminary result of this method is presented.

Field of study: Physics
Superficial fungal infection among patients with immune bullous diseases

Since no previous reported studies on superficial fungal infection (SFI) among patient with an immune bullous dermatosis exist in Libya, this study aimed to determine clinical and mycological aspects of SFI among those patients.  This study was carried out in a Bullous clinic at Tripoli Central Hospital from May 2010 to October 2010. Patients were examined clinically for evidence of SFI, and scrapings were obtained from suspicious lesions for mycological investigation.  Clinical diagnosis of SFI was made in 31/79 (39.2%) female patient cases with immune bullous diseases. Their age ranged from 28 to 80 years (40 ± 13.3 years; mean ± standard deviation) and the main age group affected was 31–40 years (51.6%). A total of 20 (64.5%) of patients had pemphigus foliaceus, 4 (12.90%) pemphigus vulgaris, 3 (9.68%) herpetiform pemphigus, 2 (6.45%) bullous pemphigoid, 1 (3.2%) pemphigus vegetans, and 1 (3.23%) had IgA pemphigus. The majority (87.1%) were living in rural area, 90% of them were homemakers, and 19.4% had a diabetes mellitus. Fingernail involvement was seen in 38.9%, and toenail and tinea pedis were seen in 25% of cases equally. Distal subungual onychomycosis was the predominant clinical entity. Direct microscopic examination was positive in 51.4% and positive culture was obtained in 54.1%. Candida species were the main isolated organism from fingernails and dermatophytes from toenails.  This study revealed that SFI was more frequent among female patients with pemphigus foliaceus and Candida species was the main isolated organism from the fingernails.

Field of study: Medicine
Interaction energies between glycopeptide antibiotics and substrates in complexes determined by X-ray crystallography: application of a theoretical databank of aspherical atoms and a symmetry-adapted perturbation theory-based set of interatomic potentials.

Intermolecular interaction energies between fragments of glycopeptide antibiotics and small peptide ligands are evaluated using geometries determined by X-ray crystallography and recently developed methods suitable for application to very large molecular complexes. The calculation of the electrostatic contributions is based on charge densities constructed with a databank of transferable aspherical atoms described by nucleus-centered spherical harmonic density functions, and uses the accurate and fast EPMM method. Dispersion, induction and exchange-repulsion contributions are evaluated with atom-atom potentials fitted to intermolecular energies from SAPT (symmetry-adapted perturbation theory) calculations on a large number of molecules. For a number of the complexes, first-principle calculations using density functional theory have been performed for comparison. Results of the new methods agree within reasonable bounds with those from DFT calculations, while being obtained at a fraction (less than 1%) of the computer time. A strong dependence on the geometry of the interaction is found, even when the number of hydrogen bonds between the substrate and antibiotic fragment is the same. While high-resolution X-ray data are required to obtain interaction energies at a quantitative level, the techniques developed have potential for joint X-ray/energy refinement of macromolecular structures.

Field of study: Chemistry
Xeroderma Pigmentosum C (XPC) Mutations in Primary Fibroblasts Impair Base Excision Repair Pathway and Increase Oxidative DNA Damage

Xeroderma Pigmentosum C (XPC) is a multi-functional protein that is involved not only in the repair of bulky lesions, post-irradiation, via nucleotide excision repair (NER) per se but also in oxidative DNA damage mending. Since base excision repair (BER) is the primary regulator of oxidative DNA damage, we characterized, post-Ultraviolet B-rays (UVB)-irradiation, the detailed effect of three different XPC mutations in primary fibroblasts derived from XP-C patients on mRNA, protein expression and activity of different BER factors. We found that XP-C fibroblasts are characterized by downregulated expression of different BER factors including OGG1, MYH, APE1, LIG3, XRCC1, and Polβ. Such a downregulation was also observed at OGG1, MYH, and APE1 protein levels. This was accompanied with an increase in DNA oxidative lesions, as evidenced by 8-oxoguanine levels, immediately post-UVB-irradiation. Unlike in normal control cells, these oxidative lesions persisted over time in XP-C cells having lower excision repair capacities. Taken together, our results indicated that an impaired BER pathway in XP-C fibroblasts leads to longer persistence and delayed repair of oxidative DNA damage. This might explain the diverse clinical phenotypes in XP-C patients suffering from cancer in both photo-protected and photo-exposed areas. Therapeutic strategies based on reinforcement of BER pathway might therefore represent an innovative path for limiting the drawbacks of NER-based diseases, as in XP-C case.

Field of study: Biology
Code switching and collusion: Classroom interaction in Botswana primary schools

The hierarchical values attached to languages in Botswana are reflected in educational policy: English occupies a prestigious position as the language of education beyond Standard 4, whereas Setswana and other indigenous languages are marginalized. Code switching by Standard 6 teachers is meant to encourage participation by pupils. However, pupils may not switch from English (the “on-stage” language). They are merely actors in the joint “staging” of ritualised question-and answer performances—as directors and co-actors teachers have access to Setswana (the “backstage” language). Some accounts claim that traditional cultural patterns of interaction underlie these institutionalised recitation routines. I argue instead that it derives from conventions imposed during colonial rule, including the requirement to use a foreign language in the classroom. Code switching in my data offers insights into the collusion of teachers and pupils in mutual face-saving over the adequacy of their classroom interaction for the achievement of teaching and learning.

Field of study: Education, Linguistics
Different spatio-temporal expressions of three otx homeoprotein transcripts during zebrafish embryogenesis.

Three zebrafish otx homeoproteins containing a homeodomain homologous to that of the Drosophila orthodenticle head gap gene product have been identified by cloning and sequencing of cDNAs. The zebrafish otx2 homeoprotein shares high amino-acid sequence identity with the mouse Otx2 homeoprotein, whereas the zebrafish otx1 and otx3 homeoproteins exhibit moderate homology with the mouse Otx1 and Otx2 homeoproteins. Three otx homeoprotein mRNAs show different spatio-temporal expression patterns during zebrafish embryogenesis as revealed by Northern blot and whole mount in situ hybridization analyses. Large amounts of the otx1 homeoprotein mRNA are found in fertilized uncleaving eggs. The otx3 homeoprotein mRNA appears in the embryonic shield, the site of the organizer. In the developing brain, three zebrafish otx mRNAs are distributed in the diencephalon and the midbrain, but their fine expression patterns are different. These results suggest that three zebrafish otx homeoproteins, alone or in combination, may play roles in very early embryogenesis, gastrulation, and the development and subdivision of the diencephalon and the midbrain.

Field of study: Biology
Wind erosion and its impact on off-site air quality in the Columbia Plateau ― an integrated research plan

With the advent of the 1990 Clean Air Act came the responsibility to monitor and control fugitive air particulates with diameters less than 10 micron (10 ¥ 10–6-m, PM10). Many urban areas, particularly in the Western United States, have experienced concentrations of these particulates which exceeded the federal health standards of this legislation a sufficient number of days that costly remedial measures have been required. In several of these cases, it has been evident that a significant amount of this material was generated by wind erosion on upwind agricultural fields, entrained in the regional air mass, and impacted downwind urban areas. There is an urgent need to better define the hazards and controls of PM10 particulate material emitted by wind erosion on agricultural lands. It is not possible with current knowledge to determine the quantity of PM10 material emitted from agricultural areas or to prescribe appropriate control methods. An extensive research and evaluation plan has been developed and initiated for the Columbia Plateau of Eastern Washington State with multi-disciplinary and multi-agency involvement.

Field of study: Agricultural and Food sciences
Towards investigation of the inhibitor-recognition mechanisms of drug-target proteins by neutron crystallography.

It is generally known that enzymes represent important drug-target proteins. Elucidation of the catalytic function and the molecular-recognition mechanisms of enzymes provides important information for structure-based drug design. Neutron crystallography provides accurate information on the locations of H atoms that are essential in enzymatic function and molecular recognition. Recent examples are described of the structure determination of the drug-target proteins human immunodeficiency virus protease and porcine pancreatic elastase in complex with transition-state analogue inhibitors using the neutron diffractometers for biological crystallography (BIX-3 and BIX-4) installed at the JRR-3 research reactor.

Field of study: Chemistry
Traffic Engineering for wireless connectionless access networks supporting QoS-demanding media applications

This paper focuses on the problem of optimal QoS Traffic Engineering (TE) in Co-Channel Interference (CCI)-affected power-limited wireless access networks that support connectionless services. By exploiting the analytical tool offered by nonlinear optimization and following the emerging ''Decomposition as Optimization'' paradigm , the approach pursued in this paper allows to develop a resource allocation algorithm that is distributed, asynchronous, scalable and self-adaptive. Interestingly, the proposed algorithm enables each node of the network to distribute its outgoing traffic among all feasible next-hops in an optimal way, as measured by an assigned global cost function of general form. This optimal traffic distribution complies with several subjective as well as objective QoS requirements advanced by the supported media flows and involves only minimum information exchange between neighboring nodes. Furthermore, it allows for load-balanced multiple forwarding paths and it is able to self-perform optimal traffic re-distribution (i.e., re-routing) in the case of failure of the underlying wireless links. Finally, actual effectiveness of the overall proposed algorithm is numerically tested via performance comparisons against both DSDV-based single-path routing algorithms and interference-aware multipath routing algorithms.

Field of study: Computer science
Behavioral Activation for Moderately Depressed University Students: Randomized Controlled Trial

Although depression is prevalent among university students, limited and dated research has examined theefficacy of behavioral interventions in treating this population (C. Lee, 2005). On the basis of a modifiedversion of the Behavioral Activation Treatment for Depression (BATD; D. R. Hopko & C. W. Lejuez,2007; C. W. Lejuez, D. R. Hopko, & S. D. Hopko, 2001) that involved a structured single-sessionintervention and 2-week treatment interval, the authors conducted a randomized controlled trial com-paring individualized BATD and a no-treatment control for university students with moderate depressionsymptoms ( N 30). Outcome measures assessed depression, environmental reward, social support, andsomatic anxiety. Relative to the control group, repeated measures analyses of variance and reliablechange indices indicated that the BATD group had significantly greater reductions in depression andincreased environmental reward at post-treatment that were associated with strong effect sizes. Astatistical trend suggested that BATD also may show promise toward increasing social support. Givencurrent conditions in many academic institutions that include high demand for mental health services,limited personnel, and time restrictions, brief and parsimonious interventions like BATD may representa viable treatment option. Study limitations and future directions are discussed. behavioral activation, college students, depression, treatment outcome

Field of study: Psychology
Superconductor digital receiver components

We have developed and experimentally demonstrated several new RSFQ circuits, designed as components for digital receivers that are being developed by HYPRES. The first circuit is a digital phase generator, which produces a periodic digital signal with a controllable phase shift. This signal is obtained by decimation of an external high frequency signal by a factor of 1024, and provides a controllable phase shift with digital precision of /spl pi//512. The second circuit, a precise digital static frequency divider, is capable of dividing of an input signal frequency by any integer value between 1 and 1024. The third circuit is a digital quadrature mixer performing digital downconversion of bit-stream data. This report presents results of experimental evaluation of these circuits at speeds in excess of 30 GHz.

Field of study: Physics
Antimitochondrial autoantibodies in anti‐glomerular basement membrane disease

Anti‐glomerular basement membrane (GBM) disease is characterized by the production of an autoantibody with very restricted specificity, with no evidence of polyclonal B cell activation. It was therefore surprising to find that in a solid‐phase ELISA a proportion of anti‐GBM sera showed significant binding to pyruvate dehydrogenase (PDH), a reactivity usually associated with the antimitochondrial autoantibodies (AM A) found in primary biliary cirrhosis (PBC). The specificity of this reactivity was confirmed by inhibition and competition experiments. The AMA found in anti‐GBM sera were of much lower affinity than those found in PBC sera, and recognized a more restricted set of species (mainly the 55‐kD and occasionally the 74‐kD component of PDH). However, it was possible to block the binding in a Western blot of an anti‐GBM serum to both the 55‐kD and 74‐kD species with F(ab')2 fragments prepared from a PBC serum. Although AMA have been found in diseases other than PBC, such diseases have usually been characterized by polyclonal B cell activation. The stimulus to the production of AMA in anti‐GBM disease, and their significance in pathogenesis (if any), are unknown.

Field of study: Biology, Medicine
Consumption decisions under uncertainty

Publisher Summary This chapter discusses three issues related to consumption decisions under uncertainty, namely, the determinants of risk aversion for future consumption, the impact of uncertainty about future resources on current consumption, and the separability of consumption decisions and portfolio choices. These issues are discussed in the context of a simple model introduced, together with the assumptions, in the chapter. The chapter presents a derivation of a (local) measure of risk aversion for delayed risks which, like the Pratt measure in the timeless context, represents twice the risk premium per unit of variance for infinitesimal risks. The aversion for delayed risks grows as curvature of the indifference loci increases, or consumers who would respond strongly to a (compensated) change in the rate of interest are relatively better suited to carry delayed risks.

Field of study: Economics
Outcomes of the SCS project and their applicability to multilateral cooperative initiatives for the management of coastal seas and marine basins

This paper summarizes the benefits of experience gained through the execution of the South China Sea project that offer useful insights into the successful development and implementation of similar multilateral interventions for environmental protection and remediation in other coastal and regional sea waters. These benefits fall into several categories: political commitment, management framework, cooperative arrangements; transparency; and scientific veracity. Experience gained in each of these categories during the South China Sea project is outlined to provide an exemplar for the successful formulation and implementation of similar interventions in other regional marine areas.

Field of study: Environmental science
Expression, purification, crystallization and preliminary X-ray analysis of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.

A recombinant form of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (E.C. 3.2.2.9) has been purified to homogeneity and crystallized using the hanging-drop vapour-diffusion technique. While several different crystallization conditions were obtained, only one set of conditions yielded crystals suitable for X-ray diffraction analysis. These crystals grow as diamond-shaped wedges, with unit-cell parameters a = 50.92, b = 133.99, c = 70.88 A, alpha = beta = gamma = 90 degrees. The crystals belong to space group P2(1)2(1)2 and diffract to a minimum d spacing of 2.3 A on a MAR345 image plate with a Rigaku RU-200 rotating-anode X-ray generator. On the basis of density calculations, two monomers are predicted per asymmetric unit (Matthews coefficient, V(M) = 2.37 A(3) Da(-1)), with a solvent content of 48%.

Field of study: Chemistry