nils-herrmann/clean_scirepeval huggingface dataset:
Development of the open‐source dose calculation and optimization toolkit matRad

We report on the development of the open‐source cross‐platform radiation treatment planning toolkit matRad and its comparison against validated treatment planning systems. The toolkit enables three‐dimensional intensity‐modulated radiation therapy treatment planning for photons, scanned protons and scanned carbon ions.  matRad is entirely written in Matlab and is freely available online. It re‐implements well‐established algorithms employing a modular and sequential software design to model the entire treatment planning workflow. It comprises core functionalities to import DICOM data, to calculate and optimize dose as well as a graphical user interface for visualization. matRad dose calculation algorithms (for carbon ions this also includes the computation of the relative biological effect) are compared against dose calculation results originating from clinically approved treatment planning systems.  We observe three‐dimensional γ‐analysis pass rates ≥ 99.67% for all three radiation modalities utilizing a distance to agreement of 2 mm and a dose difference criterion of 2%. The computational efficiency of matRad is evaluated in a treatment planning study considering three different treatment scenarios for every radiation modality. For photons, we measure total run times of 145 s–1260 s for dose calculation and fluence optimization combined considering 4–72 beam orientations and 2608–13597 beamlets. For charged particles, we measure total run times of 63 s–993 s for dose calculation and fluence optimization combined considering 9963–45574 pencil beams. Using a CT and dose grid resolution of 0.3 cm3 requires a memory consumption of 1.59 GB–9.07 GB and 0.29 GB–17.94 GB for photons and charged particles, respectively.  The dosimetric accuracy, computational performance and open‐source character of matRad encourages a future application of matRad for both educational and research purposes.

Field of study: Medicine, Physics
Clinical Profile of Primary Headaches and Awareness of Trigger Factors in Migraine Patients

To classify the patients as per the International Classification of Headache disorders 3rd edition Beta version. To study the demographic details and clinical profile. To study the trigger factors in migraine patients. To study the importance of family history is headache patients.  The study was a cross sectional observational study of 300 patients at outpatient clinic tertiary health care center, over a period of two years. Patients diagnosed with primary headache were studied with help of an exhaustive questionnaire which covered the relevant details.  Our study had 158 migraines (MG), 137 Tension Type Headache (TTH) and 5 Trigeminal Autonomic Cephalgia (TAC) patients. Females are more affected, 1:2.9 in TTH and 1:1.5 in MG. Mean age for MG was 33.37 and for TTH were 36.11. Majority (46-48%) were employed, followed by housewives (43-38%) and students (9-13%) among both the groups. TTH patients had frequency of headache more patients than migraine patients. Family history was positive in 36% in MG and 14% in TTH patients. TTH had dull aching, holocranial pain with pericranial tenderness; whereas migraine had throbbing unilateral pain. Aura was seen only in 21% of MG patients; retinal (67%) being most common. Associated symptoms like nausea, phonophobia, photophobia were seen in 80% of MG patients. Trigger factors on history were present in 64%, which increased to 85% on showing detail list. Most common triggers were climatic, followed by travel, stress and sleep related. Females had hormonal, smell and emotional stress as more common TF.  Migraine is most common primary headache presenting in clinics. With predominance in females TTH attacks are more frequent than migraine. TTH showed features like dull aching, pressure like and holocranial pain whereas migraine has throbbing and unilateral pain. Pericranial tenderness is more in TTH patients whereas migraine has associated vasomotor symptoms. It is important to have detail list of all Trigger factors for Migraine patients, so that they can avoid them and prevent their attacks, thus reducing analgesic use. Family history has more influence in migraine patients compared to TTH.

Field of study: Medicine
Interlacing molecular threads on transition metals

Copper(1) is ideally adapted to a three-dimensional template effect allowing interlacing of 1,lO-phenanthroline based molecular threads. By using appropriate cyclization procedures, interlocked macrocyclic ligands, the catenands, were prepared via the intermediate synthesis of their corresponding copper(1) complexes, the catenates. Systems containing two and three interlocked rings were made. Catenands display very special coordinating properties, allowing in particular to strongly stabilize low formal oxidation states (for instance, a Ni(1) catenate is air stable) and photo-excited states. A -catenand (consisting of three interlocked coordinating rings) contains two potential complexing sites. Hetero-dinuclear compounds have been made : Cu(I)-Ag(I) and Cu(1)-Co(I1). Electrochemical studies show the two complex subunits to strongly interact, the mode of interaction probably involving intramolecular stacking between aromatic rings of the ligands rather than direct communication between the metals. If directed rings are employed, the catenands and catenates synthesized present novel properties : the systems obtained are topologically chiral. By using two copper(1) centers as templating species and by entwining two bis-chelating threads around them in the proper fashion, a double helix is obtained. It leads after cyclization to a dicopper complex molecular trefoil knot which can be demetalated to a knotted free macrocyclic ligand. The synthesis of catenanes (interlocked rings) and knots has been a highly challenging problem to chemists for several decades (ref. 1,2). Such molecular systems  are fascinating both for their aesthetic aspect and for their intriguing topological properties. Chemical topology was initiated in 1961 by the publication of an important article in which the notion of topological isomers was introduced (ref. 1). The archetypal system of topological isomerism is that of the trefoil knot and the unknotted ring, as depicted in Fig. 2. Catenane Knot Unknotted ring Knots Fig. 1 Fig. 2. Topological stereoisomers. A s discussed more recently (ref. 3 ) , the three hypothetical molecules of Fig. 2 are

Field of study: Chemistry
The Usage of the Preposition “yu” in The Analects of Confucius

This article mainly inspects the syntactic function and grammatical meaning of the preposition structure which is composed by the preposition "yu" in The Analects of Confucius.Syntactically,this structure mainly serves as complement in sentences while as adverb in a few cases.In the aspect of grammatical meaning,the structure is mainly used to present the connecting object,express location and cope in fewer cases and introduce patient and indicate time and passivity occasionally.

Field of study: Agricultural and Food sciences
Research of Biroller Casting and Rolling AZ91D Semi-solid Magnesium Alloy Strip

Experimental study on the twin roll semi-solid strip casting and rolling of AZ91D magnesium alloy was carried out using twin roll caster.Semi-solid slurry preparation has been analyzed,and the optimal operating parameters,such as the melting temperature and the casting speed were examined.With mechanical milling at about 590 ℃,it was casting and rolling at 550～(585 ℃).The result shows that the technology of semi-solid strip casting and rolling can improve plastic processing property and refine grain.In addition,the maximal reduction arrived 46% when the magnesium alloy has been hot rolled at 380 ℃.

Field of study: Materials science
A preliminary evaluation of some elements for designation of preservation and impact reference zones in deep sea in the Clarion-Clipperton Zone: A case study of the China ocean mineral resources association contract area

At present, the enthusiasm for deep-sea mining is increasing in major countries worldwide. However, the impact of deep-sea mining on the environment is not clearly understood. The International Seabed Authority (ISA) has issued a series of regulations on mining environmental management. Environmental baseline data collection, impact reference zones (IRZs) and preservation reference zones (PRZs) designation, and an Environmental Impact Assessment (EIA) for test mining are required during the exploration period, which also provides support for environmental management during exploitation periods in the future. This study presents a process based on some environmental and biological elements that can be used to guide the preliminary designation of Reference Zones (RZs) (IRZ and PRZ) in the Clarion-Clipperton Zone, using the COMRA contract area as a case study. Based on the monitoring results in the initial RZs of the COMRA contract area, we compare the similarities of hydrological, chemical and biological communities feature between 3 RZs. And finally, we give suggestions on the key elements in designing the RZs. These findings provide evidence for the future development of environmental management plans for deep-sea mining by the ISA.

Field of study: Environmental science
Granulomatosis with polyangiitis (GPA) presenting as thick-walled cavitary lung lesion.

A 58-year-old female with a history of psoriatic arthritis on immunosuppressive therapy presented to the clinic with flu-like symptoms, cough, and blood-tinged sputum for one week. She denied chills, night sweats, wheezing, chest pain, weight loss, joint pain, or muscle aches. She had smoked for 31 pack-years and quit 1 year earlier. She was born and lived in upstate New York with no previous exposure to tuberculosis (TB). She had no exposure to chemicals or bird or bat droppings. There was no recent history of travel to any fungal endemic areas. Her home medications included albuterol, fluticasone-salmeterol, montelukast, omeprazole and citalopram. Her physical examination was completely normal, and she had a white blood cell count of 13.8 10/l with a platelet count of 63 10/ml. She was prescribed amoxicillin/clavulanate for presumed pneumonia. Because of the persistence of symptoms, imaging studies were done. Chest x-ray showed a cavitary lesion with an air-fluid level in the right upper lobe (Figure 1A ). Computed tomography of the chest demonstrated a cavitary mass with irregular thick walls and air-fluid level, as well as a 1.1 0.8 cm rounded subpleural nodule in the anterior left upper lobe . Bronchoscopic washings were negative for malignancy and infectious workup for bacteria including TB and fungi were negative. Biopsy of the left lung nodule showed extensive necrotizing suppurative granulomatous inflammation consistent with granulomatosis with polyangiitis. Her proteinase 3 ANCA levels were also elevated which supported the diagnosis. The patient was started on rituximab and prednisone with improvement in her symptoms. Differential diagnosis of a cavitary lesion in the lung is broad. Infectious causes include bacterial pathogen, fungal or TB infection. Noninfectious causes include malignancy and systemic inflammatory diseases, such as rheumatoid arthritis or granulomatosis with polyangiitis. Granulomatosis with polyangiitis is a multisystem disease that involves multiple organs especially the lungs and kidneys. The frequent lung manifestations are nodules and infiltrates. Cavitation of the nodules occurs in 25% of nodules when they are > 2 cm, and the presentation of a solitary cavitary lesion is a rare phenomenon.

Field of study: Medicine
Recognition of porcine growth hormone by a panel of monoclonal antibodies.

A panel of murine monoclonal antibodies (MAbs) against porcine growth hormone (pGH) has been raised from BALB/c mice. MAbs were characterized for binding to growth hormones (GH), prolactins (PRL), and placental lactogen (PL) from different species and to the N-terminal peptides of GH. From their patterns of cross-reactivity MAbs were assigned into nine specificity groups. The sharing of pGH epitopes among hormones of different species was related to the sequence similarity to pGH, i.e., overlap was greatest for equine, ruminant, and rodent GHs and least for human GH, ovine, and porcine PRLs, and human PL. Partial epitope mapping was carried out by relating hormone cross-reactivity patterns with amino acid sequences. Two epitopes were localized to interhelical loops, around valine-73 and glycine-130, respectively. Direct mapping with synthetic peptides localized other epitopes (Groups 7, 8, and 9) to the N-terminal region of the GH molecule. Selected MAbs were studied for the enhancement of the somatogenic activity of pGH in the dwarf mouse bioassay, measuring weight gain and sulphate incorporation into costal cartilage. Only those antibodies with specificities for GHs and not PRL or PL showed significant enhancement in this assay.

Field of study: Biology
Estimation of SCRAM Rate Trends in Nuclear Power Plants Using Hierarchical Bayes Models

Nuclear reactors are equipped with reactor scram systems to ensure rapid shutdown of the system in the event of leaks, failure of power conversion systems, or other operational abnormalities. The U.S. Nuclear Regulatory Commission (NRC) collects data on scram rates from various nuclear power plants over time to estimate the trend of proper functioning of the plants which in turn is used to regulate them. The annual scram data obtained from 66 commercial nuclear power plants indicate an increase in the number of plants having no scrams from 1.5% in 1986 to 33% in 1993. To analyze correlated count data with excess zeros (e.g., no scrams), a zero-inflated model that accounts for both temporal and plant-to-plant variation is being developed in this article. A wide class of possibly non-nested models was fitted using Markov Chain Monte Carlo (MCMC) methods and compared using a predictive criterion. Out-of-sample tests were also performed to study the performance of the models in predicting the scram rates of the plants. For the NRC data on scram rates, the stochastic time trend models that account for zero-inflation were found to provide a much better fit compared to the deterministic trend models.

Field of study: Mathematics
CURVE FITTING OF THE FATIGUE CRACK GROWTH CHARACTERRISTIC OF METALS

In this paper, a new curve fitting approach to the fatigue crack growth characteristic of metals is developed, in which modified hyperbolic functions are employed. Based on the of fatigue crack growth testing data of 2024-T42 aluminum alloy, a curve fitting analysis of the fatigue crack growth characteristic is conducted and the fatigue crack growth rate and the fatigue life are given. Compared with experimental data, the results of the present curve fitting approach are shown to be accurate.

Field of study: Engineering
BRIEF COMMUNICATIONS: Influence of the coherence length of radiation on phase noise in a fiber-optic rotation sensor

An investigation was made of a fiber-optic rotation sensor with a semiconductor light source. The length of a single-mode fiber waveguide was 1 km, its linear losses were ~ 2 dB/km at λ = 0.84 μ, the coil diameter was 19 cm, and the sensitivity of the sensor was 0.5 deg/h (1.1 × 10−5 rad) for an integration time of 0.5 sec. The drift of the zero setting in 80-min operation was ~ 6 deg/h when the fiber waveguide coil was screened from external magnetic fields and the integration time was 1 sec. A comparison was made with a similar rotation sensor based on a He–Ne laser. A new method for suppressing nonreciprocal phase noise by a vibration device simulating the Sagnac phase shift in a wide spectral range was proposed and demonstrated.

Field of study: Engineering, Physics
Jeab at 50: coevolution of research and technology.

Evidence of how behavioral research and technology have evolved together abounds in the history of the Journal of the Experimental Analysis of Behavior (JEAB). Technology from outside the discipline (exogenous), from such disciplines as electronics and computer science, has been adapted for use in behavioral research. Technology from within the discipline (endogenous) has developed from both basic behavioral research and existing apparatus. All of these sources of technology have contributed to the corpus of behavioral research as it has evolved in JEAB. Such research, in turn, has provided the environmental pressure necessary for continuing technological evolution both within and outside the discipline. The new technology thus evolved further spurs research along in novel directions. This dynamic coevolutionary interplay between research and technology is an important variable in the past, present, and future of JEAB.

Field of study: Biology, Psychology
Solid Electrolyte Nanometer Switch

We have investigated solid-electrolyte switches that utilize electrochemical reactions (deposition and dissolution) of metallic ions. The switch turns off or on when a metallic bridge electrochemically forms or dissolves in the solid electrolyte. Each state is nonvolatile and the switching is repeatable up to 105 cycles. The promising application is a programmable switch in a field programmable logic because of its small size (< 30 nm) and low ON-resistance (< 100Ω). In this paper, we will discuss the electrical characteristics, operation principle, and applications of the solid electrolyte switch.

Field of study: Computer science
Mineralization of p-nitrophenol by a new isolate Arthrobacter sp. Y1

Arthrobacter sp. Y1, capable of metabolizing p-nitrophenol (PNP) as the sole carbon, nitrogen and energy source was isolated from activated sludge. The bacterium could tolerate concentrations of PNP up to 600 mg L− 1, and degradation of PNP was achieved within 120 h of incubation. PNP and its metabolites were analyzed by high performance liquid chromatography (HPLC). The metabolite formed indicated that the organism followed the 4-nitrocathechol (4-NC) pathway for metabolism of this compound. The relevant degrading-enzyme was extracellular. Addition of other carbon source (glucose 0∼ 30 g L− 1) led to accelerated degradation. If the glucose concentration exceeded 30 g L− 1, however, degradation was repressed. Spectrophotometry assay of the nitrite and genotoxic study showed that strain Y1 could detoxify PNP. Therefore, the present study may provide a basis for the development of the bioremediation strategies to remedy the pollutants in the environment.

Field of study: Agricultural and Food sciences
Trapping phenomena in AlGaN and InAlN barrier HEMTs with different geometries

Trapping effects were evaluated by means of pulsed measurements under different quiescent biases for GaN/AlGaN/GaN and GaN/InAlN/GaN. It was found that devices with an AlGaN barrier underwent an increase in the on-resistance, and a drain current and transconductance reduction without measurable threshold voltage change, suggesting the location of the traps in the gate-drain access region. In contrast, devices with an InAlN barrier showed a transconductance and a decrease in drain associated with a significant positive shift of threshold voltage, indicating that the traps were likely located under the gate region; as well as an on-resistance degradation probably associated with the presence of surface traps in the gate-drain access region. Furthermore, measurements of drain current transients at different ambient temperatures revealed that the activation energy of electron traps was 0.43 eV and 0.38 eV for AlGaN and InAlN barrier devices, respectively. Experimental and simulation results demonstrated the influence of device geometry on the observed trapping effects, since devices with larger gate lengths and gate-to-drain distance values exhibited less noticeable charge trapping effects.

Field of study: Materials science
Gait variability and reliability after controlled tripping in older adults: a preliminary study

Approximately 21% of the falls in older adults occur due to tripping, while walking. Despite the low variability of the gait kinematic parameters within a day, there is a paucity of information regarding the variability and reliability when a tripping is induced in different days. Additionally, studies that analyzed reproducibility measures in laboratory-induced trips included only young subjects.  To analyze the variability and the reliability (intra- and inter-day) of spatiotemporal gait parameters and joint angles after controlled tripping in older adults.  Eight healthy older women performed 10-15 gait trials before and after tripping-induced laboratory in two different days. The trip was induced during the early-mid swing phase on the transposing segment and the kinematic data was obtained from trials. The variability and reliability of spatiotemporal gait parameters and joint were checked through the coefficient of variation (CV) and intraclass coefficient correlation (ICC). The two-way repeated measures ANOVA was applied.  The spatiotemporal variability was low intra and inter-day (CV: 1-4%; ICC: -0.44-0.97), whereas joint angles variability was higher (CV: 2-33%; ICC: 0.16-0.97). The variables did not differ significantly through instants and days, excepting the stride time (1%).  The spatiotemporal gait parameters and joint angles after controlled tripping in older adults present low variability and high reliability intra- and inter-day. The experimental procedures were deemed not to affect gait pattern within and between sessions.

Field of study: Education
Hill-climbing particle swarm optimization algorithm with variable width neighborhood and its application

This paper proposes a hill-climbing particle swarm optim ization algorithm with variable width neighborhood (vwnHCPSO).The new method ass umes that some stochastic particles are produced in an initial neighborhood of t he best particle P_g at the first iteration of PSO.Then the best individual P_gn of the stochastic particles is found. If P_gn is better than P_g,P_g is replaced with P_gn and the next iteration of PSO goes on. If P_gn is not better than P_g,the neighborhood wid th of the best particle P_g is broadened, the stochastic particles producti on is renewed and the best individual P_gn of stochastic particles is f ound again. If P_gn can be better than P_g now, P_g is repla ced with P_gn and the next iteration of PSO can go on. Otherwise, the neighborhood width of the best particle P_g is broadened again and the next iteration of PSO does not go on until the best individual P_gn of stoc hastic particles is found or the neighborhood width exceeds the scheduled width . Then, vwnHCPSO, hill-climbing particle swarm optimization algorithm with inv ariable width neighborhood (HCPSO) and PSO are used to resolve several well-kno wn and widely used test functions’ optimization problems. Results show t hat vwnHCPSO has greater efficiency, better performance and more advantages in m any aspects than HCPSO and PSO. Next, vwnHCPSO is used to train artificial neur al network (NN) to construct a practical soft-sensor of light diesel oil flash point of the main fractionator of fluid catalytic cracking unit (FCCU).The obtai ned results and comparison with actual industrial data indicate that the new met hod proposed in this paper is feasible and effective in soft-sensor of light di esel oil flash point.

Field of study: Chemistry, Environmental science
Inhibitory effects of tetrandrine on Bay k 8644-stimulated contraction of isolated rabbit aortic strips.

In the presence of KCl 19 mmol.L-1, calcium agonist Bay k 8644 0.47 mumol.L-1 elicited a strong contraction of isolated rabbit aortic strips, and this contraction was concentration-dependently inhibited by tetrandrine; but this antagonism was noncompetitive. Calcium ionophore calcimycin evoked contraction was markedly depressed by tetrandrine. The results suggested that tetrandrine might not only inhibit transmembrane influx of calcium via potential-dependent channels but also interfere with other processes related to calcium.

Field of study: Biology, Chemistry, Medicine