nils-herrmann/clean_scirepeval huggingface dataset:
Neurotransmitters and memory: role of cholinergic, serotonergic, and noradrenergic systems.

In Alzheimer's disease (AD), pathological changes are found in the basal forebrain cholinergic system (BFCS), serotonergic raphe (RA), and noradrenergic locus coeruleus (LC) systems. The present study was designed to determine the extent to which selective damage in each of these systems individually could produce an impairment of memory, one of the clinical symptoms of AD. Rats were given selective lesions by injecting ibotenic acid into the nucleus basalis magnocellularis and medial septal area (i.e., BFCS); 5,7-dihydroxytryptamine into the medial and dorsal RA; and 6-hydroxydopamine (6-OHDA) into the LC or by ip injections of (2-chloroethyl)N-ethyl-2-bromobenzylamine HCl (DSP4). Levels of choline acetyltransferase (ChAT), norepinephrine, and serotonin verified lesion effectiveness and selectivity. Chronic changes in serotonergic-2 and beta-adrenergic receptors were also determined. Rats were tested in a delayed spatial alternation in a T-maze. BFCS lesions impaired choice accuracy with intertrial delays of 5, 30, and 60 s. RA lesions or DSP4 injections impaired choice accuracy only when the intertrial delay was 60 s. LC lesions (by 6-OHDA) did not impair choice accuracy at any delay. The results suggest that the pathological changes in the BFCS and RA are sufficient to produce the types of memory impairments associated with dementia, but the quantitative effects of pathology in these two systems are different.

Field of study: Biology, Psychology
Respectfulness from the patient perspective: comparison of primary healthcare evaluation instruments.

Respectfulness is one measurable and core element of healthcare responsiveness. The operational definition of respectfulness is "the extent to which health professionals and support staff meet users' expectations about interpersonal treatment, demonstrate respect for the dignity of patients and provide adequate privacy."



To examine how well respectfulness is captured in validated instruments that evaluate primary healthcare from the patient's perspective, whether or not their developers had envisaged these as representing respectfulness.



645 adults with at least one healthcare contact with their own regular doctor or clinic in the previous 12 months responded to six instruments, two subscales that mapped to respectfulness: the Interpersonal Processes of Care, version II (IPC-II, two subscales) and the Primary Care Assessment Survey (PCAS). Additionally, there were individual respectfulness items in subscales measuring other attributes in the Components of Primary Care Index (CPCI) and the first version of the EUROPEP (EUROPEP-I). Scores were normalized for descriptive comparison. Exploratory and confirmatory (structural equation modelling) factor analyses examined fit to operational definition.



Respectfulness scales correlate highly with one another and with interpersonal communication. All items load adequately on a single factor, presumed to be respectfulness, but the best model has three underlying factors corresponding to (1) physician's interpersonal treatment (eigenvalue=13.99), (2) interpersonal treatment by office staff (eigenvalue=2.13) and (3) respect for the dignity of the person (eigenvalue=1.16). Most items capture physician's interpersonal treatment (IPC-II Compassionate, Respectful Interpersonal Style, IPC-II Hurried Communication and PCAS Interpersonal Treatment). The IPC-II Interpersonal Style (Disrespectful Office Staff) captures treatment by staff, but only three items capture dignity.



Various items or subscales seem to measure respectfulness among currently available validated instruments. However, many of these items related to other constructs, such as interpersonal communication. Further studies should aim at developing more refined measures - especially for privacy and dignity - and assess the relevance of the broader concept of responsiveness.

Field of study: Medicine, Political science
Nanopore Sequencing and De Novo Assembly of a Black-Shelled Pacific Oyster (Crassostrea gigas) Genome

The Pacific oyster, Crassostrea gigas, belongs to one of the most species-rich phyla and provides important ecological and economical services. Here we present a genome assembly for a variety of this species, black-shelled Pacific oyster, using a combination of 61.8 Gb Nanopore long reads and 105.6 Gb raw BGI-seq short reads. The genome assembly comprised 3,676 contigs, with a total length of 587 Mb and a contig N50 of 581 kb. Annotation of the genome assembly identified 283 Mb (48.32%) of repetitive sequences and a total of 26,811 protein-coding genes. A long-term transposable element active, accompanied by recent expansion (1 million years ago), was detected in this genome. The divergence between black-shelled and the previous published Pacific oysters was estimated at about 2.2 million years ago, which implies that species C. gigas had great intraspecific genetic variations. Moreover, we identified 148/188 specifically expanded/contracted gene families in this genome. We believe this genome assembly will be a valuable resource for understanding the genetic breeding, conservation, and evolution of oysters and bivalves.

Field of study: Biology
Complexity Economics as Heterodoxy: Theory and Policy

Complexity economics has quickly become a powerful research program for real-world economics in recent years. This article provides an overview of complexity economics, and argues that it is incompatible with the “equilibrium” and “optimality” conceptions of the mainstream and its “market economy.” Instead, it develops older heterodox — including evolutionary-institutional — issues like self-organization, emergence, path‑dependence, idiosyncrasies, lock-ins, or skewed power distributions. Also, the space for emergent institutions through the “intentionality” of agents, including their improving collective performance, reducing complexity, and others, is investigated. This article considers complex adaptive systems through “games on networks” in an “evolution-of-cooperation” perspective. Moreover, a surge in policy implications of economic complexity has emerged, even if still rather general. With some more specific implications derived, the article again reveals the close similarities with long-standing heterodoxies: namely, pragmatist policy conceptions in this respect.

Field of study: Economics
Positive integer powers of certain complex tridiagonal matrices

In this paper, we firstly present a general expression for the entries of the rth ([email protected]?N) power of a certain n-square complex tridiagonal matrix, in terms of the Chebyshev polynomials of the first kind. Secondly, we obtain a complex factorization formula for generalized Fibonacci-Pell numbers obeying also classical Fibonacci and Pell numbers.

Field of study: Mathematics
Intracerebroventricularly injected L-arginine-induced vasopressin release is mediated by cGMP in rats.

To study the possible role of cGMP in the effect of L-arginine-induced arginine-vasopressin (AVP) release.



In anesthetized rats, saline, L-arginine, 8-Br-cGMP, L-arginine + methylene blue (an inhibitor of guanylyl cyclase) were injected intracerebroventricularly (icv) and the plasma vasopressin level was detected with radioimmunoassay.



Both 8-Br-cGMP 2.53 g.L-1 and L-arginine 100 g.L-1 increased plasma AVP level [from (2.6 +/- 0.3) to (6.6 +/- 0.4) ng.L-1, and from (3.2 +/- 0.5) to (5.8 +/- 1.4) ng.L-1, respectively; P < 0.01] 5 min after the icv injection; methylene blue (3.74 g.L-1) + L-arginine (100 g.L-1) did not change plasma AVP level.



cGMP was a mediator of the effect of L-arginine-induced AVP release.

Field of study: Biology, Chemistry, Medicine
Prolonged chilling under moderate light: effect on photosynthetic activity measured with the photoacoustic method

Exposure of tomato plants to a mild chilling temperature and relatively low ambient photon flux density for an extended period (10°C and 400 μmol photons m−2 s−1 d and 5°C night for 6 d) resulted in a significant decrease in the variable chlorophyll fluorescence, the quantum yield of oxygen evolution and the amount of total absorbed energy stored in photochemical intermediates, but not in the chlorophyll concentration or in the activity of ribulose biphosphate carboxylase. These results indicate that photochemical processes involving PSII were affected, and might reflect photoinhibitory effects on the photosynthetic apparatus. 
 
Chilling treatment had relatively small influence on the maximal extent of the Emerson effect. This observation, together with the sharp decrease found in the quantum yield of oxygen evolution, could be reconciled with the above results only if some dependency between the two photosystems was assumed. On the basis of this interpretation, it was concluded that the strong Emerson effect after chilling still reflects the typical imbalance between PSI and PSII centres, even though populations of such unaffected pairs are smaller than in the untreated plants. 
 
The relatively new photoacoustic technique employed in this study is shown to be useful both as a diagnostic tool and as a means of investigating changes in photochemical activity in the study of environmental stress effects on photosynthesis. The results support the view that photoinhibition can play an important role in limiting photosynthetic activity, and therefore productivity, in chilling-sensitive plants such as the tomato under the natural conditions that prevail during the winter in mediterranean climates.

Field of study: Environmental science
Bifungites, trace fossils from Devonian-Mississippian rocks of Pennsylvania and Montana, U.S.A

The trace fossil Bifungites Desio 1940, first recognized in Late Devonian rocks of Libya and later in Algeria, is common in Late Devonian rocks of Montana, Pennsylvania, Ohio, and Michigan, and Early Mississippian rocks of Pennsylvania. Its manifestations are given for seven stratigraphic units from forty localities in Pennsylvania, Montana, and Michigan. Bifungites commonly occur on bedding planes and consist of a horizontal shaft with doubly terminating arrow- or dumb-bell-shaped projections. Less apparent are paired vertical cylindrical sediment-filled tubes connected at their base to the bi-arrow or dumb-bell shaft. The combination represents the mud or silt casting of an inverted pi-shaped, μ, infaunal tubular burrow (domichnia). Siltstone slabs have been transversely sectioned to reveal this π-shaped, double-arrow burrow pattern with undisturbed stratification between the vertical tubes. Three new ichnospecies are proposed based on markedly different size and shape of the fossil traces in three stratigraphic zones. A Late Devonian Girard Shale type is the smallest with wide, short arrows on a narrow shaft whose median overall length is 12.5 mm. The latest Devonian Sappington type has well-formed, shortly barbed arrow terminations and median length of 28 mm. An Early Mississippian Meadville type is the largest with median length of 36 mm and prominently barbed broad arrows. The Bifungites organism is unrecognized but it was probably a sedentary, soft-bodied, infaunal suspension-feeding animal inhabiting shallow nearshore marine and brackish water environments. The identified biota directly or indirectly associated with Bifungites is extremely limited to a few brachiopods, clams, and other trace fossils.

Field of study: Environmental science, Geography
The Pre-College Student Science Training Program of the National Science Foundation: An Empirical Analysis

The effects of a summer science program for high school students was evaluated using matched longitudinal data from two national samples of students. Among white students of both sexes, participation in the program appears to increase interest in majoring in science in college, in pursuing a career as a scientist, and in going on for the PhD. degree. Although similar, but less pronounced, effects were observed among black male participants, no such effects were observed among black female participants.

Field of study: Education
The Technical Child: In Vitro Fertilization and the Personal Subject

Two moral issues of our day have captured much public attention: abortion and embryonic stem cell research. However, another issue, which is positioned precisely between these two and directly related, in vitro fertilization (lVF), has not shared the limelight to nearly the same extent. IVF is a primary source of the controversy over embryonic stem cell research and a result of legalized abortion. As such, it calls for more intense scrutiny than it has thus far received. Perhaps the pain of infertile couples desiring a child seems too delicate a matter with which to take issue. But certainly the problem of women in crisis over their pregnancy is no less delicate. Compassion calls for love grounded in truth, not shadowy obfuscation. IVF is a contemporary tragedy unfolding in our country and elsewhere in the world. This tragedy could be called "The Technical Child"." It is produced and directed by medical and research scientists and technicians. The main characters are the infertile couple, embryonic children, a doctor and his team of medical technicians, the scientific research community, and God, the Creator. To uncover the tragedy it is necessary to look at each of these as a personal subject and to examine the role they take and the actions for which they are responsible. As each character is examined, some of the realities of the IVF process will be described and the moral, theological and anthropological issues involved will be elucidated, along with some of the controversy surrounding them.

Field of study: Medicine, Philosophy
Geochronologic and isotopic evidence for Triassic-Jurassic emplacement of the eugeoclinal allochthon in the Mojave Desert region, California

The geologic history of the outer continental margin (eugeoclinal) rocks in the El Paso Mountains and northern Mojave Desert has long been important in models for the development of the active continental margin in the western Cordillera. Current interpretations call for either strike-slip or thrust juxtaposition of eugeoclinal rocks against miogeoclinal/cratonal (platformal) rocks, or some combination of both strike-slip faulting and thrusting. Two broad and interrelated aspects of the history of the eugeoclinal rocks are at issue: (1) How much primary displacement is necessary to account for the present position of the eugeoclinal rocks? and (2) When were the eugeoclinal rocks thrust against platformal rocks? This study primarily addresses the second issue. Lithologic correlation indicates that the outcrop belt of eugeoclinal rocks is bounded by platformal rocks to the east and south. Platformal rocks are also present to the west, but many of these exposures restore to a position structurally beneath the eugeoclinal rocks when Tertiary extension is restored, implying stacking by a thrust. New U-Pb zircon geochronology and whole rock geochemistry and Sr, Nd, and Pb isotopic data for plutons in the El Paso Mountains and northern Mojave Desert lend insight into the timing of this thrusting. The outcrop belt of eugeoclinal rocks coincides with the only known Permian and Triassic plutons in the El Paso Mountains and northern Mojave Desert, which are dated at 260 to 240 Ma by U-Pb zircon in this report. Initial Sr and ϵ Nd(t) isotopic values from these plutons are distinct ≤0.704 and ≥+2, respectively) from continental lithosphere isotopic signatures ≥0.705 and ≤−2) of both Middle Jurassic plutons in the same area and Triassic plutons in the southern and eastern Mojave Desert. Feldspar common lead data for the Permian and Triassic plutons within the eugeoclinal outcrop belt also indicate limited crustal involvement and do not overlap previously reported values for common lead data from Mesozoic plutons in the eastern Mojave Desert region where Proterozoic basement is widespread. The observations and data reported here indicate that Late Permian–Early Triassic plutons in the northern Mojave Desert and El Paso Mountains were generated within or passed primarily through oceanic lithosphere, but later Jurassic plutons were derived from and/or interacted extensively with continental lithosphere. We hypothesize that the eugeoclinal rocks were deposited on oceanic crust that was thrust eastward over Precambrian cratonal basement and overlying strata between approximately 240 Ma and 175 Ma, a time of little documented tectonic activity in the Mojave Desert region. Postulated Permian or late Middle Jurassic east-directed thrusting is incompatible with our data and observations. The data also fill an important gap in palinspastic reconstructions of the early Mesozoic arc and indicate that this arc was northwest-trending and oblique to Paleozoic facies trends in the Mojave Desert.

Field of study: Geology
MAGNETIC FIELD STRENGTH IN AN INTERMEDIATE-VELOCITY IONIZED FILAMENT IN THE FIRST GALACTIC QUADRANT

We investigate the magnetic field in an intermediate-velocity filament for which the Hα intensity in the WHAM survey correlates with excess Faraday rotation of extragalactic radio sources over the length of the filament from b ≈ 20° to b ≈ 55°. The density-weighted mean magnetic field is , derived from rotation measures and an empirical relation between Hα emission measure and dispersion measure from Berkhuijsen et al. In view of the uncertainties in the derived magnetic field strength, we propose an alternative use of the available data, rotation measure, and emission measure, to derive a lower limit to the Alfven speed, weighted by electron density . We find lower limits to the Alfven speed that are comparable to or larger than the sound speed in a plasma, and conclude that the magnetic field is dynamically important. We discuss the role of intermediate-velocity gas as a locus of Faraday rotation in the interstellar medium, and propose that this lower limit to the Alfven speed may also be applicable to Faraday rotation by galaxy clusters.

Field of study: Physics
Analysis of pesticide residues on museum objects repatriated to the Hupa tribe of California.

In the past, it was common practice for museum professionals and private collectors to apply a variety of pesticide agents to objects in their collections to preserve them from depredations by microorganisms, fungi, and other pests. The Native American Graves Repatriation and Protection Act allows federally recognized tribes to request that museums return objects taken from their ancestors. Given that poor records were kept on the treatment of individual objects, it is unknown whether specific objects are contaminated with these pesticide agents. Although chemical analysis represents the only reliable means to determine the types and levels of pesticides on these objects, surprisingly few publications document the extent of this contamination in museum collections. This paper reports on the determination of arsenic, mercury, and several organic pesticides on 17 objects that were recently repatriated to the Hupa tribe in northern California. Four samples were taken from each object: two for arsenic and mercury analysis via flame atomic absorption spectrophotometry and two for organic pesticide analysis via gas chromatography/mass spectrometry. Percent levels (wt/wt) of mercury were detected on many samples, and 0.001 to 0.183% (wt/wt) levels of p-dichlorobenzene, naphthalene, thymol, lindane, and/or DDT were detected on many of the samples. These results indicate that Hupa tribal members should not wear these objects in religious ceremonies, proper precautions should be followed when dealing with potentially contaminated objects, and that more serious consideration should be given to this issue at a national level.

Field of study: Environmental science
Establishment of Extraction Methods and Two-dimensional Electrophoresis Conditions for Proteomic Analysis of Camellia sinensis

In order to develop efficient two-dimensional electrophoresis(2-DE) conditions suitable for tea proteome analysis, the effects of different protein extraction methods and sample loading amount were compared. The results showed that the modified phenol extraction protocol was more suitable for total protein extraction of tea compared with trichloroacetic acid(TCA)/acetone precipitation. And loading 1.5 mg protein sample, a high quality 2-DE image map with more protein spots, clear background and high protein point resolution was obtained. The research provides a foundation for further study of tea proteomics.

Field of study: Agricultural and Food sciences
Complex maze performance in rats: effects of noradrenergic depletion and cholinergic blockade.

Noradrenergic (NA) involvement in acquisition (AQ) and retention (RET) of a shock-motivated 14-unit T-maze after intraperitoneal (ip) administration of DSP4, a neurotoxin that depletes forebrain NA, was evaluated in 2 experiments using 3-month-old male F-344 rats. Depletion of cortical NA level in DSP4-treated rats was verified by neurochemical assay and by latency to postdecapitation clonus reflex. In Experiment 1, DSP4 (50 mg/kg ip) rats did not differ from saline-treated (SAL) rats on any measure of maze performance (errors, alternation errors, run time, shock duration, or shock frequency) during AQ (DSP4 2 weeks prior to testing) nor during a RET test 2-3 weeks later (DSP4 immediately after the last AQ trial or 1 week after AQ). In Experiment 2, DSP4 and scopolamine (SCOP), a cholinergic (ACh) antagonist, were administered in combination to test for an NA-ACh interaction. DSP4 (50 mg/kg ip 2 weeks prior to AQ) again had no effect on AQ performance nor did DSP4 interact with either dose of SCOP (0.25 or 0.5 mg/kg ip 30 min prior to AQ) to further impair performance. Similar to previous studies SCOP impaired all measures of maze performance except shock duration. These experiments provide further evidence for involvement of ACh systems in the learning of this task and in the age-related impairments previously observed, but they suggest that central NA systems may not be involved directly or interactively with ACh systems required for efficient performance in this maze.

Field of study: Biology, Psychology
Technical Note: Partial body irradiation of mice using a customized PMMA apparatus and a clinical 3D planning/LINAC radiotherapy system.

In vivo radiobiology experiments involving partial body irradiation (PBI) of mice are of major importance because they allow for the evaluation of individual organ tolerance; overcoming current limitations of experiments using lower dose, whole body irradiation. In the current study, the authors characterize and validate an effective and efficient apparatus for multiple animal PBI, directed to the head, thorax, or abdomen of mice.



The apparatus is made of polymethylmethacrylate and consists of a rectangular parallelepiped prism (40 cm × 16 cm × 8 cm), in which five holes were drilled to accomodate standard 60 ml syringes, each housing an unanesthetized, fully immobilized mouse. Following CT-scanning and radiotherapy treatment planning, radiation fields were designed to irradiate the head, thorax, or abdomen of the animal. Thermoluminescent dosimeters (TLDs) were used to confirm the treatment planning dosimetry for primary beam and scattered radiation.



Mice are efficiently placed into 60 ml syringes and immobilized, without the use of anesthetics. Although partial rotational movement around the longitudinal axis and a minor 2 mm forward/backward movement are permitted, this does not compromise the irradiation of the chosen body area. TLDs confirmed the dose values predicted by the treatment planning dosimetry, both for primary beam and scattered radiation.



The customized PMMA apparatus described and validated is cost-effective, convenient to use, and efficient in performing PBI without the use of anesthesia. The developed apparatus permits the isolated irradiation of the mouse head, thorax, and abdomen. Importantly, the apparatus allows the delivery of PBI to five mice, simultaneously, representing an efficient way to effectively expose a large number of animals to PBI through multiple daily fractions, simulating clinical radiotherapy treatment schedules.

Field of study: Medicine, Physics