nils-herrmann/clean_scirepeval huggingface dataset:
New Pathogenic Germline Variants in Very Early Onset and Familial Colorectal Cancer Patients

A genetic diagnosis facilitates personalized cancer treatment and clinical care of relatives at risk, however, although 25% of colorectal cancer cases are familial, around 95% of the families are genetically unresolved. In this study, we performed gene panel analysis on germline DNA of 32 established or candidate colorectal cancer predisposing genes in 149 individuals from either families with an accumulation of colorectal cancers or families with only one sporadic case of very early onset colorectal cancer (≤40 years at diagnosis). We identified pathogenic or likely pathogenic genetic variants in 10.1% of the participants in genes such as APC, POLE, MSH2 or PMS2. The MSH2 variant, c.2168C>T, p.(Ser723Phe) was previously described as a variant of unknown significance, but we have now reclassified it to be likely pathogenic. The POLE variant, c.1089C>A, p.(Asn363Lys) was identified in a patient with three metachronous colorectal cancers from age 28 and turned out to be de novo. One pathogenic PMS2 variant was novel. We also identified a number of highly interesting variants of unknown significance in APC, BUB1, TP53 and RPS20. The RPS20 variant is novel and was found in a large Amsterdam I positive family with a multi tumor phenotype including 12 cases of CRC from as early as age 24. This variant was found to segregate with cancer in the family and multiple in silico tools predict it to be pathogenic. Our data further support the shift from phenotypic-based cancer panels to large panels including all established genes involved in hereditary cancer syndromes or (targeted) whole genome sequencing. Additionally, identification of a likely disease-predisposing variant in RPS20 expands the phenotypic spectrum of RPS20-related cancers and emphasize that this gene is relevant to include in colorectal cancer gene panels.

Field of study: Biology
Clinical Study of Acute Intestinal Obstruction

Acute intestinal obstruction is one of the most common surgical emergencies. There are many causes of acute intestinal obstruction like bands and adhesions, neoplasms, strictures etc.  In this study we have tried to find out common clinical presentation, aetiology and treatment of acute intestinal obstruction.  This is a prospective study conducted at department of General Surgery, Dr. Vasantrao Pawar Medical College, Hospital and Research Centre, Nashik, Maharashtra in which we have studied 45 cases of acute intestinal obstruction to find out the clinical presentation, aetiology and treatment of acute intestinal obstruction.  Acute intestinal obstruction is more common in females than in males. Small intestinal obstruction is more common than large intestinal obstruction. The commonest cause of intestinal obstruction is adhesions. The next most common cause is Tubercular stricture. Malignancy is most common cause of large intestinal obstruction. Most of the patients having large bowel obstruction required laparotomy.

Field of study: Medicine
An iterative scheme for signal settings and network flows

An area traffic control optimization is considered where the signal setting variables and link flows are simultaneously determined. The optimal signal settings and network flows (OPSF) can be formulated as a mathematical program with equilibrium constraints (MPEC) where the user equilibrium is expressed as a variational inequality problem. Due to the non-differentiability of the perturbed solutions in equilibrium constraints, a non-smooth model is established. A Quasi–Newton subgradient projection is presented to effectively solve the OPSF with global convergence. Numerical calculations are conducted on an example network where promising results are obtained.

Field of study: Mathematics
Biologically inspired protection of deep networks from adversarial attacks

Inspired by biophysical principles underlying nonlinear dendritic computation in neural circuits, we develop a scheme to train deep neural networks to make them robust to adversarial attacks. Our scheme generates highly nonlinear, saturated neural networks that achieve state of the art performance on gradient based adversarial examples on MNIST, despite never being exposed to adversarially chosen examples during training. Moreover, these networks exhibit unprecedented robustness to targeted, iterative schemes for generating adversarial examples, including second-order methods. We further identify principles governing how these networks achieve their robustness, drawing on methods from information geometry. We find these networks progressively create highly flat and compressed internal representations that are sensitive to very few input dimensions, while still solving the task. Moreover, they employ highly kurtotic weight distributions, also found in the brain, and we demonstrate how such kurtosis can protect even linear classifiers from adversarial attack.

Field of study: Computer science
Robust Estimation of the First-Order Autoregressive Parameter

Outliers in time series can adversely affect both the least squares estimates and ordinary M-estimates of autoregressive parameters. Attention is focused here on obtaining robust estimates of the parameter for a first-order autoregressive time series xk The observations are y k = z k + v k, and two models are considered: Model IO, with v k ≡ 0, x k possibly non-Gaussian, and Model AO, with v k nonzero and possibly quite large a small fraction of the time, and x k Gaussian. A class of generalized M-estimates is proposed which has attractive mean-squared-error robustness properties towards both IO and AO type deviations from the Gaussian model.

Field of study: Mathematics
No. 44968. United Nations and Bahrain

Exchange of letters constituting an agreement between the United Nations and the Government of the Kingdom of Bahrain regarding the hosting of the 2008 Economic and Social Council Annual Ministerial Review (AMR) Regional Preparatory Meeting focusing on the theme "Sustainable Urbanization", to be held in Manama, from 1 to 2 June 2008. New York, 8 May 2008 and 22 May 2008

Field of study: Political science
The growth and characterization of (211) and (133) Oriented (Hg,Cd)Te epilayers (211)B GaAs by organometallic vapor phase epitaxy

The growth of CdTe buffer layers on (211)B GaAs substrates by organometallic vapor phase epitaxy (OMVPE) was studied, and it was found that, depending on the growth conditions, either the (211) or (133) epitaxial orientation could be formed. In some cases, an epilayer showing a mixed (211) and (133) orientation was also observed. The influence of several growth parameters on the orientation of the CdTe layer was investigated, and it was found that the Te/Cd ratio, together with the growth temperature, have the most significant effect in determining the epilayer orientation. From these results, it was then possible to select nominally optimized growth conditions for CdTe buffer layers of both orientations. (Hg,Cd)Te layers of the same orientations could then be grown and characterized. Although double crystal x-ray diffraction measurements indicated a somewhat better crystalline perfection in the (133) (Hg,Cd)Te layers, these layers showed a poor surface morphology compared to the (211) orientation. Measurement of etch pit densities also indicated defect densities to be typically half an order of magnitude higher in the (133) orientation. Diodes were formed by ion implantation in both orientations and significantly better results were obtained on the (211) (Hg,Cd)Te layers.

Field of study: Materials science
Large Flux-Mediated Coupling in Hybrid Electromechanical System With A Transmon Qubit

Control over the quantum states of a massive oscillator is important for several technological applications and to test the fundamental limits of quantum mechanics. Addition of an internal degree of freedom to the oscillator could be a valuable resource for such control. Recently, hybrid electromechanical systems using superconducting qubits, based on electric-charge mediated coupling, have been quite successful. Here, we realize a hybrid device, consisting of a superconducting transmon qubit and a mechanical resonator coupled using the magnetic-flux. The coupling stems from the quantum-interference of the superconducting phase across the tunnel junctions. We demonstrate a vacuum electromechanical coupling rate up to 4 kHz by making the transmon qubit resonant with the readout cavity. Consequently, thermal-motion of the mechanical resonator is detected by driving the hybridized-mode with mean-occupancy well below one photon. By tuning qubit away from the cavity, electromechanical coupling can be enhanced to 40 kHz. In this limit, a small coherent drive on the mechanical resonator results in the splitting of qubit spectrum, and we observe interference signature arising from the Landau-Zener-St\"uckelberg effect. With improvements in qubit coherence, this system offers a novel platform to realize rich interactions and could potentially provide full control over the quantum motional states.

Field of study: Physics
Free-radical hydroxymethylation of benzimidazole

Several benzimidazole derivatives were subjected to free-radical hydroxymethylation. Benzimidazole displays lower activity than quinoline in the first stage of the transformation, viz., in the addition of the hydroxymethyl radical. The yields of hydroxymethylation products are also determined by the ability of the intermediate benzimidazolium cation radicals to undergo oxidation and are increased in the presence of a catalyst, viz., silver ions.

Field of study: Chemistry
Synthesis of nitro- and aminoindoles

Optimal conditions are proposed for the direct nitration of 2,3-dimethylindoles containing methyl and methoxy groups in the benzene ring. In contrast to 5- and 6-methylindoles and 5- and 6-methoxyindoles, nitration of 7-methyl-and 7-methoxy-2,3-dimethylindoles proceeds differently under the same conditions. A series of previously unreported aminoindoles was obtained by reduction of the nitroindoles.

Field of study: Chemistry
What determines Orthoptera species distribution and richness in temperate semi-natural dry grassland remnants?

Wide-spread fragmentation and isolation of habitats with high nature conservation value lends increasing importance to a better understanding of the factors which determine species richness in isolated habitat patches. Using data of one of the most abundant invertebrate groups in grasslands, Orthoptera, we analysed how species richness and distribution in 60 isolated semi-natural grassland remnants in Austria were affected by five environmental variables (altitude, habitat and land use diversity within each patch, habitat diversity of areas adjacent to each patch, patch size), and related to diversity of their main food source, i.e. vascular plants. We found a significant positive correlation between Orthoptera and vascular plant species richness, with threatened Orthoptera species having the lowest correlation coefficients. Life form diversity of plants was only moderately positively correlated with Orthoptera species richness. Habitat diversity within and adjacent to the grassland patch had by far the highest loadings on the first two axes of the principal component analysis, which jointly explained 99 % of the variance, and proved to be significant for total, threatened and not threatened Orthoptera, as well as for the two Orthoptera orders occurring in Central Europe (Caelifera, Ensifera). Additionally, the distribution of the majority of those 14 Orthoptera species analysed individually was mainly correlated with habitat diversity within and adjacent to the grassland patch. However, the distribution of a significant proportion of species was associated with other factors: five species were closely related to on-site land use diversity and patch size, and the distribution of three Ensifera species was not significantly correlated to any of the explanatory variables. We conclude that a surrogate taxa approach, i.e. the use of well-known taxonomic groups (e.g. vascular plants), may indeed deliver good results for capturing total, but less so for threatened, Orthoptera species richness in semi-natural grassland remnants. Small scale habitat diversity may be crucial to allow for the co-existence of a large number of Orthoptera species and has to be taken equally into account as patch size in nature conservation.

Field of study: Environmental science
Spektren emissionsfähiger Stoffe bei Erregung durch Licht und durch chemische Reaktionen

Zusammenfassung1.Die Spektren der Chemilumineszenz und Fluoreszenz von frischem und altem Silikon wurden photographiert und ausphotometriert. Die Maxima der vergleichbaren Chemilumineszenz- und Fluoreszenzspektren sind gleich.2.Die Spektren der Fluoreszenz von Rhodamin B und Echtsäureeosin und die Spektren der Chemilumineszenz der beiden Farbstoffe, die auftreten, wenn Adsorbate derselben an ausgeleuchtetem Silikon mit KMnO4 oxydiert werden, wurden photographiert und photometriert. Die vergleichbaren Photometerkurven der Fluoreszenz und Chemilumineszenz der Farbstoffe sind gleich.3.Die Absorptionsspektren von Rhodamin und Echtsäureeosin bei Durchgang von Silikonlumineszenzlicht durch eine Lösung dieser Farbstoffe sind vollkommen verschieden von den Farbstofflumineszenzspektren.4.Die Identität der Chemilumineszenz und Fluoreszenz desselben Stoffes zeigt, daß in beiden Fällen die gleiche Emission stattfindet, und daß der Unterschied nur in der verschiedenen Art der Erregung beruht.5.Die Ergebnisse der Arbeit bestätigen die Theorie, daß Chemilumineszenz durch Übertragung der Energie von reagierenden Molekülen auf nicht reagierende emissionsfähige Moleküle zustande kommen kann.6.Es wurde nachgewiesen, daß diese Übertragung der Energie nicht durch Strahlung erfolgt.7.Die manchmal auftretende grüne (statt rote) Chemilumineszenz von Rhodamin B bei Verwendung sehr alter Silikonpräparate erklärt sich aus der Bildung von grün emittierenden Oxydationsprodukten des Rhodamins.
 Zum Schluß möchten wir Herrn Prof. Freundlich für die Förderung der Arbeit bestens danken.

Field of study: Physics
Modafinil and memory: effects of modafinil on Morris water maze learning and Pavlovian fear conditioning.

Modafinil has been shown to promote wakefulness and some studies suggest the drug can improve cognitive function. Because of many similarities, the mechanism of action may be comparable to classical psychostimulants, although the exact mechanisms of modafinil's actions in wakefulness and cognitive enhancement are unknown. The current study aims to further examine the effects of modafinil as a cognitive enhancer on hippocampus-dependent memory in mice. A high dose of modafinil (75 mg/kg ip) given before training improved acquisition on a Morris water maze. When given only before testing, modafinil did not affect water maze performance. We also examined modafinil (0.075 to 75 mg/kg) on Pavlovian fear conditioning. A low dose of pretraining modafinil (0.75 mg/kg) enhanced memory of contextual fear conditioning (tested off-drug 1 week later) whereas a high dose (75 mg/kg) disrupted memory. Pretraining modafinil did not affect cued conditioning at any dose tested, and immediate posttraining modafinil had no effect on either cued or contextual fear. These results suggest that modafinil's effects of memory are more selective than amphetamine or cocaine and specific to hippocampus-dependent memory.

Field of study: Biology, Psychology
A Study on the Influence of Brand Image on Consumers’ Purchase Intention—Based on IT Skills Training

Many IT skills training institutions in our country have ignored the creation of the image of brand in the fierce competition, which would lead to the operating crisis. This study is based on the previous research, variables and scales, and does the analysis from four aspects including corporate image, service image, humanity image and signal image, by using SPSS. According to the study, all of the corporate image, service image, humanity image and signal image have positive impact on consumer purchase intention, among which the impact of service image is largest, and that of humanity image is least.

Field of study: Engineering
Impact of irradiation and immunosuppressive agents on immune system homeostasis in rhesus macaques

In this study we examined the effects of non‐myeloablative total body irradiation (TBI) in combination with immunosuppressive chemotherapy on immune homeostasis in rhesus macaques. Our results show that the administration of cyclosporin A or tacrolimus without radiotherapy did not result in lymphopenia. The addition of TBI to the regimen resulted in lymphopenia as well as alterations in the memory/naive ratio following reconstitution of lymphocyte populations. Dendritic cell (DC) numbers in whole blood were largely unaffected, while the monocyte population was altered by immunosuppressive treatment. Irradiation also resulted in increased levels of circulating cytokines and chemokines that correlated with T cell proliferative bursts and with the shift towards memory T cells. We also report that anti‐thymocyte globulin (ATG) treatment and CD3 immunotoxin administration resulted in a selective and rapid depletion of naive CD4 and CD8 T cells and increased frequency of memory T cells. We also examined the impact of these treatments on reactivation of latent simian varicella virus (SVV) infection as a model of varicella zoster virus (VZV) infection of humans. None of the treatments resulted in overt SVV reactivation; however, select animals had transient increases in SVV‐specific T cell responses following immunosuppression, suggestive of subclinical reactivation. Overall, we provide detailed observations into immune modulation by TBI and chemotherapeutic agents in rhesus macaques, an important research model of human disease.

Field of study: Biology, Medicine
What Positive Impacts Does Peer Tutoring Have Upon The Peer Tutors at SQU

This paper attempts to provide an answer to the question: What positive impacts does peer tutoring have upon the peer tutors at SQU? It is conducted in the LC Tutorial Centre at Sultan Qaboos University where senior English language students are hired to tutor their peers who are struggling with the language. It sheds light on the peer tutors' academic, social, professional, psychological, and personal gains. Data were gathered from twenty-five currently employed peer tutors through a survey questionnaire and a group discussion. The study results prove the success of the adopted one-on-one peer-tutoring program in contributing to the peer tutors' development. The PTs benefited academically through the resources available in the TC and exchanging knowledge with their peers. They also found peer-tutoring a good chance to practice their language skills. Furthermore, the experience opened a horizon for students to expand their social network by making friendships with different students and staff. The PTs learnt to be more responsible, confident, patient, outgoing, and punctual. Most of all, the peer tutors explored the feelings of fulfillment and achievement through hearing positive feedback from their tutees and believing themselves to be productive members of SQU campus life and a reason for somebody's success in learning the English language.  Peer learning, Peer Tutoring, Peer Tutor, Tutorial, Tutorial Center, Tutor, SQU, Oman, Positive Impact, SQU, Oman.  PT (Peer tutor), SQU (Sultan Qaboos University), LC (Language Centre), SSU (Student Support Unit), TC (Tutorial Center), GPA (Grade Point Average)

Field of study: Education
SU-G-IeP1-10: Permeability Evaluation of Interstitial Cystitis by DCE-MRI of the Bladder.

Interstitial cystitis (IC) is a chronic and painful condition that can lead to bladder pain syndrome (BPS) in women. IC and BPS have been known to manifest after physiological changes after giving birth. In this project, we pioneered and advanced a new clinical utility using DCE-MRI to assess bladder permeability. At first IC/BPS perfusion methods were with ratio signal evaluation, we now incorporate pharmacokinetics techniques to allow for further assessment.



In this pilot study, female patients and volunteers (IC=4, Control=3) underwent imaging with a clinical GE 3T 750W MRI system. This project was approved by the OUHSC IRB. Multiple TR Images series were acquired. Images were analyzed in the coronal plane at 0-, 3-, 6-, 9-, 12-, 15-, 20-, 25-, and 30-minute intervals. We used a three-compartmental pharmacokinetic model with these data. The compartments included: a) bladder interior site of injection, b) bladder wall, and c) external psoas muscle. The signal was transformed and corrected for T1-relaxation based on a multi-TR exponential regression before pharmacokinetic analysis.



Significant differences (p<0.05) were detected with relative means for T1 concentration changes (IC/BPS=0.0107, control=0.616) on the outflow between the k13 transfer coefficient, which represents the injection leakage to the external parenchyma. Trend differences (p<0.1) were found in permeability between the bladder injection site to the rim. We also found changes in the kurtosis of the histograms of regional perfusion. No detectable changes were found in the reverse directions for the above compartments (k21, k31).



We report clinical changes in this pilot study. This study illustrates early detectable evidence for a possible DCE-MRI tool that can detect permeability differences with pharmacokinetics measurement of k13. These techniques are intended to advance quantitative imaging methods for IC/BPS, per the goals/objectives of the Quantitative Imaging Biomarker Alliance (QIBA) and other AAPM and RSNA initiatives.

Field of study: Medicine, Physics
On a least squares predictive-transform modeling methodology

A deterministic least squares (LS) predictive-transform (PT) multichannel modeling framework is presented. In a manner analogous to the development of minimum mean square error (MSE) PT, the LS PT signal model is obtained as an inherent byproduct of an optimized predictive-transform signal source "encoder", thereby preserving the direct integration of specific data compression concepts into the basic modeling procedure that have proven very useful in the application of minimum MSE PT to coding, detection, estimation, and control. Fundamental properties of the LS PT signal model are presented, and a recursive least squares (RLS) PT modeling procedure is developed. In addition to subsuming conventional RLS signal modeling as a special case and the presence of an integrated transformation mechanism, RLS PT offers greater flexibility when independent "fading memory" weighting of both the first- and second-order sample moments is desired. Sufficient conditions for the convergence of the RLS PT parameters to their minimum MSE PT counterparts are developed. In addition, the zero mean constraint (either deterministic or stochastic) imposed on the LS PT signal model's innovation sequence is shown to provide a mechanism for mitigating the deleterious effects of a singular or near-singular data correlation matrix.

Field of study: Engineering