nils-herrmann/clean_scirepeval huggingface dataset:
Generation of human monoclonal antibody Fab fragments against respiratory syncytial virus (RSV) using phage display technology

To develop a safe and effective medicine for RSV infection. The hu- man IgG Fab genes of heavy and light chains were amplified from peripheral lymphocytes of four infants in conva- lescent phase of asthma-like pneumonia caused by RSV infection in an outbreak in Henan province,and cloned in- to phage display system (pComb3/VCSM13).The combinatorial phage Fab antibody library was constructed and followed by screening with purified RSV virions.The specific human antibody Fab fragments against RSV were se- lected and expressed in XL1-Blu,and the specificity of the expressed RSV Fabs were characterized by ELISA.Fi- nally the sequence of Fab genes from the positive clones were analyzed by alignment with GenBank. The human antibody library consists of 10~8 independent clones.Six rounds of selection against McAb captured RSV par- ticles showed specific enrichment of phage antibodies.Direct ELISA verified that the positive phage antibodies were specific against RSV.Analysis of the DNA sequence indicates that the human immunoglobulin Fab sequence was identified and confirmed. Human IgG Fab fragments anti-RSV were obtained with phage display technique.

Field of study: Biology
Hydrogeology of the South Fork of Long Island, New York

The South Fork of Long Island, New York, is underlain by unconsolidated Pleistocene and Cretaceous sediments resting on crystalline bedrock. A two-layered aquifer system contains fresh ground water with saline ground water in the deeper strata. The average horizontal hydraulic conductivity of the upper aquifer is 49 m/day and of the lower aquifer is 25 m/day. The average annual precipitation of 1.14 m is the only natural source of fresh water. After consumptive losses the precipitation provides about 1.85 × 10 8 m 3 /yr to recharge the water table. Discharge of fresh ground water occurs primarily as undersea outflow to the ocean at the perimeter of the area. The safe yield of the area is estimated to be 9.15 × 10 4 m 3 /day.

Field of study: Geology
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of HP1352, a putative DNA methyltransferase in Helicobacter pylori.

The putative methyltransferase gene HP1352 from Helicobacter pylori strain 26695 was heterologously expressed in Escherichia coli. The 359-amino-acid gene product was purified and crystallized. The crystals belong to space group I2(1)2(1)2(1) and show diffraction to at least 2.5 A resolution. The unit-cell parameters are a = 69.6, b = 86.6, c = 140.0 A. A greater than 90% complete native data set has been collected and structure determination using the molecular-replacement method is ongoing.

Field of study: Chemistry
ASSARTING AND THE GROWTH OF THE OPEN FIELDS

C ENTRAL and eastern Yorkshire offers a uniquely suitable field for the study of certain problems of twelfthand thirteenth-century agrarian history. The basin of the Ouse, as opposed to the moors of the west and north-east, forms part of the central and eastern English plain; and of the whole region treated in the classical accounts of medieval agrarian history it is, perhaps, the only part which has not been subjected to detailed study. There is a special affinity between the plain of Yorkshire and the region between Welland and Trent ;2 that the rural organisation of Yorkshire after the Conquest has not been studied in conjunction with that of the central Danelaw is due to an event which modified, temporarily or perhaps permanently, the development of the northern district.a The devastation of io69, more extensive in some districts than in others, left about half the Yorkshire plain entirely waste in io86, and had evidently affected many districts in which the Domesday commissioners found some surviving population. There can be no doubt of the intensity and lasting effects of the devastation. In many vills, seventeen years later, no population was recorded, and no income even from woods or rough pasture ; over large parts of Yorkshire the cultivation of the soil was entirely suspended, perhaps for a generation or longer.4 It is, therefore, reasonable to look for the mature post-Conquest development of Yorkshire at a somewhat later date than for that of the region illustrated by Danelam Charters, and to place it in the thirteenth and -perhaps the late twelfth century. The evidence for this period consists chiefly of some thousands of charters surviving in various forms; and with the methods of using charter material elaborated by Professor Stenton the reader must here be assumed to be familiar. I wish to use this material at present only in so far as it relates to the distribution

Field of study: Economics, History
The Nuclear Force Problem: Is the Never-Ending Story Coming to an End?

The attempts to find the right (underlying) theory for the nuclear force have a long and stimulating history. Already in 1953, Hans Bethe stated that "more man-hours have been given to this problem than to any other scientific question in the history of mankind". In search for the nature of the nuclear force, the idea of sub-nuclear particles was created which, eventually, generated the field of particle physics. I will review this productive history of hope, error, and desperation. Finally, I will discuss recent ideas which apply the concept of an effective field theory to low-energy QCD. There are indications that this concept may provide the right framework to properly understand nuclear forces.

Field of study: Physics
Surface Acoustic Waves—A New Thin-Film Deposition Approach for Coated Conductors

A new approach for the deposition of layers for coated conductors has been developed. High-frequency surface acoustic waves (SAWs) were applied for the atomization of precursor solutions into an ultrafine aerosol. The deposition via aerosol droplet condensation offers several advantages over existing deposition methods including ink jet printing and dip coating, e.g., a variable droplet size and the possibility of gel condensation in the aerosol phase due to solvent evaporation. In the future, a combination of two or more SAW atomizers might enable the simultaneous deposition of separate solutions and even nanoparticle dispersions. First, experiments were performed using water-based and propionic-acid-based mixed lanthanum and zirconium precursor solutions. These solutions are supplied to a SAW device via a stainless steel capillary, leading to continuous aerosol production. The aerosol droplets of the precursor solution were deposited on biaxial textured Ni-5 at.%W tapes having an area of 1-cm width and about 5-cm length and were subsequently crystallized into a continuous thin La2Zr2O7 buffer layer in a tube furnace. X-ray diffraction studies showed that the La2Zr2O7 films have high crystalline quality with a strong (001)-orientation. Furthermore, microstructural analysis on the deposited films showed homogeneous and dense layers.

Field of study: Physics
Risk Factors for Acute Otitis Media in Children at Dr.Soedono Hospital

Acute otitis media (OMA) was the most common ear infection in children. Because of  Tuba Eustachius was  not developed  yet, shorter and flatter / horizontal   in children so the secretions of   nasopharynx were easier to enter the middle ear. OMA can cause many complications such as subperiosteal abscess to severe complications like meningitis and brain abscess. Epidemiological studies of OMA in developing countries were still rare. The prevalence of OMA was different in many country, ranging from 2.3 - 20%. The result of   study showed that the prevalence of OMA in children in East Jakarta was 5.38%, and the highest prevalence was on group among 2-5 years old. 179 patients analyzed  were 50.8% male and 49.2% female. The mean age of this study subjects was 4.75 years (SD 4.54). 31.3% were diagnosed with OMA. There was no difference in the location of the OMA occurrence between the right and left ear. There was a significant correlation between age factor and the incidence of OMA (p = 0.014) and subjects which under 5 years of old became a risk factor for OMA. The results also showed that there was a correlation between treatment and the incidence of OMA (p = 0.000), ARI patients without treatment was being a risk factor for the incidence of OMA in children. There was no correlation between sex, type factor and health insurance against the occurrence of OMA.

Field of study: Medicine
Efficient Blind and Partially Blind Signatures Without Random Oracles

This paper proposes a new efficient signature scheme from bilinear maps that is secure in the standard model (i.e., without the random oracle model). Our signature scheme is more effective in many applications (e.g., blind signatures, group signatures, anonymous credentials etc.) than the existing secure signature schemes in the standard model such as the Boneh-Boyen [6], Camenisch-Lysyanskaya , Cramer-Shoup  and Waters  schemes (and their variants). The security proof of our scheme requires a slightly stronger assumption, the 2SDH assumption, than the SDH assumption used by Boneh-Boyen. As typical applications of our signature scheme, this paper presents efficient blind signatures and partially blind signatures that are secure in the standard model. Here, partially blind signatures are a generalization of blind signatures (i.e., blind signatures are a special case of partially blind signatures) and have many applications including electronic cash and voting. Our blind signature scheme is much more efficient than the existing secure blind signature schemes in the standard model such as the Camenisch-Koprowski-Warinsch  and Juels-Luby-Ostrovsky [22] schemes, and is also almost as efficient as the most efficient blind signature schemes whose security has been analyzed heuristically or in the random oracle model. Our partially blind signature scheme is the first one that is secure in the standard model and it is very efficient (almost as efficient as our blind signatures). We also present a blind signature scheme based on the Waters signature scheme.

Field of study: Computer science, Mathematics
Performance evaluation of web service response time probability distribution models for business process cycle time simulation

The adoption of Business Process Management (BPM) is enabling companies to improve the pace of building new capabilities, enhancing existing ones, and measuring process performance to identify bottlenecks. It is essential to compute the cycle time of the process to assess the performance of a business process. The cycle time typically forms part of service level agreements (SLAs) and is a crucial contributor to the overall user experience and productivity. The simulation technique is versatile and has broad applicability for determining realistic cycle time using historical data of web service response time. BPM tools offer inadequate support for modeling input data used in simulation in the form of descriptive statistics or standard probability distributions like normal, lognormal, which results in inaccurate simulation results.  We evaluate the effectiveness of different parametric and non-parametric probability distributions for modeling data of web service response time. We further assess how the choice of probability distribution impacts the accuracy of the simulated cycle time of a business process. The work is the first of such a study using real-world data for encouraging Business Process Simulation Specification (BPSim) standard setters and BPM tools to enhance their support for such distributions in their simulation engine.  We consider several parametric and non-parametric distributions and explore how well these distributions fit web service response time from extensive public and a real-world dataset. The cycle time of the business process of a real-world system is simulated using the identified distributions to model the underlying web service data.  Our results show that kernel distribution is the most suitable choice, followed by Burr. Kernel outperforms Burr by 86.63% for the public and 84.21% for the real-world dataset. The choice of distribution affects the percentile ranks like 90 and above than the median. The use of single-point values underestimates cycle time values at higher percentiles.  Based on our empirical results, we recommend the addition of kernel and Burr to the current list of distributions supported by BPSim and BPM tools.

Field of study: Computer science, Engineering
Fever produced by intrahypothalamic injection of interleukin-1 and interleukin-6.

Pure human interleukin-1 beta (IL-1 beta) and interleukin-6 (IL-6), both of natural origin, were found to cause fever in rabbits when injected into the PO/AH region of the brain. The threshold dose required for this effect was between 0.4 and 4 U, equivalent to 0.04 to 0.4 ng for IL-1 beta, and around 50 U, equivalent to 0.05 ng for IL-6. From this it was estimated that this area of the brain responds to a local concentration of approximately 1 ng/ml of these cytokines, a level which can easily be reached after intravenous administration of threshold pyrogenic doses of either cytokine. The observation supports the view that fever induced by systemic endogenous production of IL-1 and IL-6 is due to a direct effect on the thermoregulatory center and may not require production of mediators, such as prostaglandins, at sites distant from the center.

Field of study: Medicine
Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.

Despite the DNA duplex being central to biological functions, many intricacies of this molecule, including the dynamic nature of mismatched base pairing, are still unknown. The unique conformations adopted by DNA mismatches can provide insight into the forces at play between nucleotides. Moreover, DNA-binding proteins apply their own individualized steric and electrochemical influences on the nucleotides that they interact with, further altering base-pairing conformations. Here, seven X-ray crystallographic structures of the human nuclease apurinic/apyrimidinic (AP) endonuclease 1 (APE1) in complex with its substrate target flanked by a 5' mismatch are reported. The structures reveal how APE1 influences the conformations of a variety of different mismatched base pairs. Purine-purine mismatches containing a guanine are stabilized by a rotation of the guanine residue about the N-glycosidic bond to utilize the Hoogsteen edge for hydrogen bonding. Interestingly, no rotation of adenine, the other purine, is observed. Mismatches involving both purine and pyrimidine bases adopt wobble conformations to accommodate the mismatch. Pyrimidine-pyrimidine mismatches also wobble; however, the smaller profile of a pyrimidine base results in a gap between the Watson-Crick faces that is reduced by a C1'-C1' compression. These results advance our understanding of mismatched base pairing and the influence of a bound protein.

Field of study: Chemistry
Solar semidiurnal tides in the troposphere : Detection by radar profilers

A short review of solar semidiurnal atmospheric tides is presented. Semidiurnal atmospheric tides have been documented in the troposphere primarily through analyses of long time series of surface pressure measurements, although the winds produced by these tides have, by now, been well documented in the middle and upper atmosphere. Recent research using UHF and very-high-frequency radar wind profilers has now identified tidal wind perturbations in tropospheric data. This review focuses on the tidal wind characteristics and the distinctive signature of this wind system in radar profiler data analyses.

Field of study: Environmental science
Learning the Structure for Structured Sparsity

Structured sparsity has recently emerged in statistics, machine learning and signal processing as a promising paradigm for learning in high-dimensional settings. All existing methods for learning under the assumption of structured sparsity rely on prior knowledge on how to weight (or how to penalize) individual subsets of variables during the subset selection process, which is not available in general. Inferring group weights from data is a key open research problem in structured sparsity. In this paper, we propose a Bayesian approach to the problem of group weight learning. We model the group weights as hyperparameters of heavy-tailed priors on groups of variables and derive an approximate inference scheme to infer these hyperparameters. We empirically show that we are able to recover the model hyperparameters when the data are generated from the model, and we demonstrate the utility of learning weights in synthetic and real denoising problems.

Field of study: Engineering
Additive regression model for stationary and ergodic continuous time processes

The main purpose of the present work is to introduce and investigate a simple kernel procedure based on marginal integration that estimates the regression function for stationary and ergodic continuous time processes in the setting of the additive model introduced by Stone (1985). We obtain the uniform almost sure consistency with exact rate and the asymptotic normality of the kernel-type estimators of the components of the additive model. Asymptotic properties of these estimators are obtained, under mild conditions, by means of martingale approaches. Finally, a general notion of the bootstrapped additive components, constructed by exchangeably weighting sample, is presented.

Field of study: Mathematics
Cultural ecosystem values of the Kimberley coastline: An empirical analysis with implications for coastal and marine policy

Cultural ecosystem services have received increasing attention in land/marine use planning but remain poorly known, expressed, and utilised in planning processes. Progress in marine spatial planning requires better information regarding the full range of values and benefits received from ecosystem services, including cultural ecosystem values. This paper reports on an online Public Participation GIS (PPGIS) study that collected spatially explicit information on cultural ecosystem values in the remote Kimberley coastal region in northwestern Australia. The coastal zone – 20 km landwards and seawards – was found to be highly valued with values disproportionally located 0–2 km onshore. The number of value markers placed was related to tenure, access (i.e., density of tracks), population density, and geomorphology. Methodologically, Public Participation GIS describes the location and extent of values providing for the exploration of relationships between values and other planning features such as tenure and coastal access. Inclusion of such information in marine spatial planning and policy formulation can contribute to more thoughtful and inclusive decisions regarding the future of coastal zones. The use of internet-based Public Participation GIS is particularly useful for long, remote coastlines with widely dispersed stakeholder interests where other methods such as interviews and workshops are not feasible.

Field of study: Environmental science
Extended experience with the use of botulinum toxin a in children with overactive bladder (OAB)

In a pilot study we showed promising results for injections with botulinum toxin A in children with a therapy resistant overactive bladder. After this retrospective study we decided to continue with a prospective uncontrolled evaluation in the pediatric age group. The results are given and discussed.  Children with a history of therapy resistant diurnal and/or nocturnal incontinence based on urodynamically proven detrusor overactivity with normal bladder emptying were included. Children were treated under general anesthesia. A dose of 100 IU botulinum toxin A (Botox®, Allergan) diluted in 20 ml normal saline was injected. Both becoming dry and changing from day and nighttime incontinence to monosymptomatic enuresis were considered successful treatment.  Seventy five patients met the inclusion criteria of which were 48 males and 27 females. Mean age at start of therapy was 112 months (9.3 years). The average follow-up was 17,37 months. Fifty eight children suffered day and night time incontinence, 5 suffered diurnal incontinence, 10 suffered nocturnal enuresis and 2 had giggle-incontinence. For the whole study group the mean voided volume increased from 176 ml to 245 ml after the first injection (p   Botulinum toxin A injection seems a safe and efficient treatment for children suffering OAB. Further studies are needed.

Field of study: Medicine
Role of the 5' enhancer of the glutamine synthetase gene in its organ-specific expression.

In mammals, glutamine synthetase (GS) is expressed in a large number of organs, but the precise regulation of its expression is still obscure. Therefore a detailed analysis of the activity of the upstream regulatory element of the GS gene in the transcriptional regulation of its expression was carried out in transgenic mice carrying the chloramphenicol acetyltransferase (CAT) gene under the control of the upstream regulatory region of the GS gene. CAT and GS mRNA expression were compared in liver, epididymis, lung, adipocytes, testis, kidney, skeletal muscle and gastrointestinal tract, both quantitatively by ribonuclease-protection analysis and topographically by in situ hybridization. It was found that the upstream regulatory region is active with respect both to the level and to the topography of GS gene expression in liver, epididymis, gastrointestinal tract (stomach, small intestine and colon) and skeletal muscle. On the other hand, in the kidney, brain, adipocytes, spleen, lung and testis, GS gene expression is not or only partly regulated by the 5' enhancer. A second enhancer, identified within the first intron, may regulate GS expression in the latter organs. Furthermore, CAT expression in the brain did not co-localize with that of GS, showing that the 5' regulatory region of the GS gene does not direct its expression to the astrocytes.

Field of study: Biology, Computer science
Reparation and Retribution: Are They Reconcilable?

The recent history of criminal justice contains an apparent anomaly: the simultaneous renaissance of retributive and reparative models of justice. This article will explore the genesis and competing claims of these two models, how it is that their fortunes have coincided, and with what consequences. Many writing in this field have felt driven to champion the claims of one or the other.’ Some of these writings read like missionary tracts whose proselytising purposes tend to obstruct measured analysis. Yet the greatest possibilities for illuminative debate have arisen where rival champions have entered into battle with one another to expose the inadequacies or undesirability of the other’s model. The consequence, however, is that positions have become polarised. Retributive and reparative justice are posed as antinomies whose claims rival one another and whose goals must be in conflict. The most radical writers propose a major paradigm shift in which reparation would take priority over punishment as the goal of the criminal justice ~ y s t e m . ~ From the opposing camp, adherents of retributivism generally argue that reparation is merely incidental to the main purpose of punishment. According to this latter view, the place of reparation within the criminal justice system serves pragmatic purposes but is conceptually anomalous. More recently, welcome attempts to bridge the gap traditionally posed between reparation and retributivism have been mooted by those who question the usefulness of this dichotomised approach to penal theory .4

Field of study: Law
Magnetic freezeout effect in Al0.32Ga0.68As

The behaviour of the thermal ionization energy of the Gamma effective-mass state under a magnetic field has been studied near the Gamma -L-X crossover of AlGaAs. The results deviate significantly from the typical behaviour and it is shown that a better agreement can be obtained if screening effects and an anticrossing with a resonant state of a1 symmetry are considered.

Field of study: Materials science