nils-herrmann/clean_scirepeval huggingface dataset:
Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results

Marker gene sequencing of the rRNA operon (16S, 18S, ITS) or cytochrome c oxidase I (CO1) is a popular means to assess microbial communities of the environment, microbiomes associated with plants and animals, as well as communities of multicellular organisms via environmental DNA sequencing. Since this technique is based on sequencing a single gene, or even only parts of a single gene rather than the entire genome, the number of reads needed per sample to assess the microbial community structure is lower than that required for metagenome sequencing. This makes marker gene sequencing affordable to nearly any laboratory. Despite the relative ease and cost-efficiency of data generation, analyzing the resulting sequence data requires computational skills that may go beyond the standard repertoire of a current molecular biologist/ecologist. We have developed Cascabel, a scalable, flexible, and easy-to-use amplicon sequence data analysis pipeline, which uses Snakemake and a combination of existing and newly developed solutions for its computational steps. Cascabel takes the raw data as input and delivers a table of operational taxonomic units (OTUs) or Amplicon Sequence Variants (ASVs) in BIOM and text format and representative sequences. Cascabel is a highly versatile software that allows users to customize several steps of the pipeline, such as selecting from a set of OTU clustering methods or performing ASV analysis. In addition, we designed Cascabel to run in any linux/unix computing environment from desktop computers to computing servers making use of parallel processing if possible. The analyses and results are fully reproducible and documented in an HTML and optional pdf report. Cascabel is freely available at Github: https://github.com/AlejandroAb/CASCABEL.

Field of study: Biology
Re-storying marine conservation: Integrating art and science to explore and articulate ideas, visions and expressions of marine space

Art-science collaborations are proliferating as the benefits of bringing artists and scientists together are increasingly recognised and supported. This paper documents an example of an artist and scientist with overlapping (as opposed to the more usual mutually exclusive) practices, in terms of artistic and scientific approaches to the research material. It illustrates how a collaboration between a marine social scientist (the author) and a visual artist helped to inspire a different approach to a marine protected area dispute between the Scottish Government and the small Scottish island community of Barra, Outer Hebrides, Scotland. The art-science collaboration resulted in Sea Stories, an interactive, online, cultural map of the sea around the island of Barra. The participatory mapping process to create the Sea Stories map involved visions and expressions of marine space being constructed through constant interaction between the research team and research participants. It revealed different ways of knowing the marine environment, hitherto not visible or acknowledged within the marine policy environment where the protection of biological diversity was the focus. The acknowledgement of a rich and diverse cultural heritage bound up with the marine biological diversity opened up possibilities for the design of a community-led and government-supported co-management process that recognises the social relations which form part of the island’s socio-ecological system.

Field of study: Environmental science
The Historiography of the Río de la Plata Area Since 1830

Two traditions have dominated the Rio de la Plata area since the colonial period.t One has been characterized by a strong liberal tendency, by its stress on freedom for the individual under elected civilian governments, by an anti-clerical (but not anti-religious) outlook, and has looked to France, England and the United States for inspiration in achieving the area's destiny. The other tradition, at times, has gone to the extremes of conservatism with its generally pro-clerical outlook and preference for Spain and the area 's own past as its guideline to the future; and in the name of "order" has been willing to accept an authoritarian government, under a man on horseback if necessary, with strict limits set on the exercise of individual liberties. This tradition has had its greatest strength in the interior, where until late in the nineteenth century local caudillos employed their gaucho followings to defy the authority of the national governments in Buenos Aires and Montevideo. The liberal tradition has had its principal following in the urban areas, particularly in

Field of study: History
Influence of gate oxides with high thermal conductivity on the failure distribution of InGaAs-based MOS stacks

In this work, the breakdown transients of metal-oxide-semiconductors (MOS) stacks with InGaAs channels and different oxide layers (Al2O3, HfO2 and Si3N4) have been studied in terms of the time-to-breakdown and the duration of the progressive breakdown regime. It is observed that dielectric layers with higher thermal conductivity show larger transient time during the progressive breakdown regime, and this provides a significant lifetime extension across the entire failure distribution. This is attributed to a lower temperature of the percolation path which reduces local electro-migration. Moreover, the overall results show that the progressive breakdown regime is uncorrelated with the initial degradation rate, and that the bending of failure distribution at low percentiles is exclusively attributed to the progressive increase of the gate current during the breakdown event.

Field of study: Engineering
Clinical characteristics and outcomes in elderly patients undergoing transsphenoidal surgery for nonfunctioning pituitary adenoma.

Life expectancy has increased over the past century, causing a shift in the demographic distribution toward older age groups. Elderly patients comprise up to 14% of all patients with pituitary tumors, with most lesions being nonfunctioning pituitary adenomas (NFPAs). Here, the authors evaluated demographics, outcomes, and postoperative complications between nonelderly adult and elderly NFPA patients.



A retrospective review of 908 patients undergoing transsphenoidal surgery (TSS) for NFPA at a single institution from 2007 to 2019 was conducted. Clinical and surgical outcomes and postoperative complications were compared between nonelderly adult (age ≥ 18 and ≤ 65 years) and elderly patients (age > 65 years).



There were 614 and 294 patients in the nonelderly and elderly groups, respectively. Both groups were similar in sex (57.3% vs 60.5% males; p = 0.4), tumor size (2.56 vs 2.46 cm; p = 0.2), and cavernous sinus invasion (35.8% vs 33.7%; p = 0.6). Regarding postoperative outcomes, length of stay (1 vs 2 days; p = 0.5), extent of resection (59.8% vs 64.8% gross-total resection; p = 0.2), CSF leak requiring surgical revision (4.3% vs 1.4%; p = 0.06), 30-day readmission (8.1% vs 7.3%; p = 0.7), infection (3.1% vs 2.0%; p = 0.5), and new hypopituitarism (13.9% vs 12.0%; p = 0.3) were similar between both groups. Elderly patients were less likely to receive adjuvant radiation (8.7% vs 16.3%; p = 0.009), undergo future reoperation (3.8% vs 9.5%; p = 0.003), and experience postoperative diabetes insipidus (DI) (3.7% vs 9.4%; p = 0.002), and more likely to have postoperative hyponatremia (26.7% vs 16.4%; p < 0.001) and new cranial nerve deficit (1.9% vs 0.0%; p = 0.01). Subanalysis of elderly patients showed that patients with higher Charlson Comorbidity Index scores had comparable outcomes other than higher DI rates (8.1% vs 0.0%; p = 0.006). Elderly patients' postoperative sodium peaked and troughed on postoperative day 3 (POD3) (mean 138.7 mEq/L) and POD9 (mean 130.8 mEq/L), respectively, compared with nonelderly patients (peak POD2: mean 139.9 mEq/L; trough POD8: mean 131.3 mEq/L).



The authors' analysis revealed that TSS for NFPA in elderly patients is safe with low complication rates. In this cohort, more elderly patients experienced postoperative hyponatremia, while more nonelderly patients experienced postoperative DI. These findings, combined with the observation of higher DI in patients with more comorbidities and elderly patients experiencing later peaks and troughs in serum sodium, suggest age-related differences in sodium regulation after NFPA resection. The authors hope that their results will help guide discussions with elderly patients regarding risks and outcomes of TSS.

Field of study: Medicine
Holocene environmental history of a peatland in the Lena River valley, Siberia

A 3.86 m core of peat and organic lake mud from a polygonal peatland in the Lena River valley of Siberia was radiocarbon dated and analyzed for pollen, plant macrofossils, chrysophyte stomatocysts, stable isotopes, and charcoal. At around 7200 BP, a shallow lake or open-water wetland supported diverse aquatic macrophytes. The site had transformed initially into a richer fen with Carex, Comarum palustris, and Drepanocladus and later a poorer fen with Sphagnum which persisted until around 3000 BP. Fire may have been responsible for silt being blown onto the peatland, which changed the hydrological and geochemical conditions for development of the poor fen. Ice accretion led to an increase in the height of the centre of the polygon and expansion of Sphagnum peatland . 18 O values become progressively more enriched, which reflects more direct input of summer precipitation waters and less groundwater during this period. Finally, the peatland surface was elevated sufficiently to limit water and nutrient supply, thereby allowing Ericaceae and Betula to grow at the coring site. Fire burned the peatland surface and may have exaggerated the extremely slow rate of peat accumulation. Fire may also be a factor in maintaining the open Larix dahurica forest in the region today, while climate may be contributing to reducing postfire regeneration. Fire and climate together may be controlling the character and composition of forests near tree line in the Lena River valley of this part of Siberia. Resume : Une carotte de tourbe et de boue organique lacustre diune longueur de 3,86 m prOlevOe dans une tourbire polygonale dans la vallOe de la rivire Lena, en SibOrie, a OtO datOe au radiocarbone et analysOe pour les pollens, plantes

Field of study: Environmental science
In Servitio Dei: Fray Diego de Landa, the Franciscan Order, and the Return of the Extirpattion of Idolatry in the Colonial Diocese of Yucatán, 1573–1579*

“My dear spiritual brothers and fathers, you whose relationship to me is closer than that of my own blood. . . . Even though my present position as Bishop might appear to separate me from you, I swear that it cannot divide me from you, because I have and always will be a son of our Father Saint Francis. . . . Now that I have returned, I come to you not as bishop, but rather as a son of this holy province into whose brotherhood I once again seek to incorporate myself. . . .” —Fray Diego de Landa, October 1573 (Spoken before the Franciscan congregation of friars in Mérida upon his arrival as the second bishop of Yucatán) “And of the idolatries that there were, I say that those who have procured to discover these idolatries and expose them and with great zeal for the honor of God those who look for idolatry and denounce it to the judges so that they can be punished, they are none other than the same religious friars of the order of Saint Francis . . .” —Bishop of Yucatán, Diego Vazquez de Mercado, 1603 On the afternoon of June 15, 1574, the conflict between the Franciscan Order and the local governor of the province of Yucatán intensified. A heated controversy had emerged between the recently appointed bishop of Yucatán, Fray Diego de Landa, and the provincial governor, Francisco Velázquez de Gijón. On that afternoon, the dean of the cathedral of Mérida, Licenciado Cristobal de Miranda, went to the home of the provincial governor with a message from the bishop. The governor had recently received an order of excommunication issued by the bishop for his actions against several Franciscan friars.

Field of study: History
Construction of a T-DNA Insertion Mutant Library of Magnaporthe grisea and Identification of Pathogenicity-related Mutants

According to the transformation system established by our laboratory, Magnaporthe grisea strain Y34 was mutated through T-DNA insertion mediated by Agrobacterium tumefaciens strain AGL-1. The transformation efficiency was 300 transformants per 1.0 ×106 conidia of the fungus on average, and 6 855 transformants were obtained. PCR amplification found that all tested transformants were resistant to hygromycin and contained hph gene, indicating that the transformants were T-DNA inserted mutants. DNA Southern blot analysis of 56 T-DNA inserted mutants indicated that the copy number of T-DNA insertion was 1.43, and that 27 mutants were single-copy insertions. Pathogenicity test of randomly selected 1 600 transformants found that 23 mutants completely lost their virulence on a susceptible rice cultivar.

Field of study: Agricultural and Food sciences
Supporting English-Language Learners in Social Studies Class: Results from a Study of High School Teachers

Content-area instruction for English-language learners (ELLs) represents a growing area of instructional need in U.S. high schools. In this article, the authors focus on diverse approaches to developing an effective instructional environment for teaching secondary-level social studies curriculum to ELLs. The authors participated in a school-university partnership to support content-area teachers' efforts to increase ELLs' comprehension skills. The authors propose a multitiered approach to meet the needs of ELLs in the mainstream social studies classrooms by (1) providing social and cultural support during the process of acculturation, (2) providing explicit instruction in academic strategies necessary for successful comprehension of in-depth content using the Cognitive Academic Language Learning Approach, and (3) making social studies curriculum more accessible through strategies for reducing cognitive load without reducing content.

Field of study: Sociology
A Chiral “Frozen” Hydrogen Bonding in C4-Symmetric Inherently Chiral Resorcin[4]arenes: NMR, X-ray, Circular Dichroism, and Theoretical Study (Eur. J. Org. Chem. 18/2008)

The cover picture shows the X-ray structure of CC4-symmetric, chiral resorcinarene substituted with L-leucine at the upper rim. The molecule is held in the inherently chiral conformation (resembling a chiral CC4-symmetric propeller) by means of twelve intramolecular hydrogen bonds. The seams of hydrogen bonds can be directed in one particular direction because of diastereomeric preferences. The determination of the direction of the hydrogen-bonding seam and the correlation with CD spectra is discussed in the article by A. Szumna et al. on p. 3069 ff.

Field of study: Chemistry
The Case for Temporal Transparency: Detecting Policy Change Events in Black-Box Decision Making Systems

Bringing transparency to black-box decision making systems (DMS) has been a topic of increasing research interest in recent years. Traditional active and passive approaches to make these systems transparent are often limited by scalability and/or feasibility issues. In this paper, we propose a new notion of black-box DMS transparency, named, temporal transparency, whose goal is to detect if/when the DMS policy changes over time, and is mostly invariant to the drawbacks of traditional approaches. We map our notion of temporal transparency to time series changepoint detection methods, and develop a framework to detect policy changes in real-world DMS's. Experiments on New York Stop-question-and-frisk dataset reveal a number of publicly announced and unannounced policy changes, highlighting the utility of our framework.

Field of study: Computer science
Symmetry Tests in Polarized Z0 Decays to bbg

Angular asymmetries have been measured in polarized Z0 decays to bbg collected by the SLD experiment at the SLC. 
A high purity bbg event sample is selected by utilizing B lifetime information given by the SLD CCD pixel vertex detector and the stable micron-size SLC beams, and the b- and bbar-jets are identified using lifetime information and momentum-weighted track charge. 
The forward-backward asymmetry is observed in the b-quark polar angle distribution, and the parity-violation parameter is measured to test the Standard Model. 
Two angular correlations between the three-jet plane and the Z0 polarization are studied. 
The CP-even and T-odd, and the CP-odd and T-odd, angular asymmetries are sensitive to physics beyond the Standard Model. The latter requires tagging both the b- and bbar-jet. We measure the expectation values of these quantities to be consistent with zero and set limits on the correlations at the 5% level.

Field of study: Physics
Kenneth Boulding: Economics from a Different Perspective

Among economists, Kenneth Boulding is one of the most imaginative, stimulating, creative, and prolific.' He views much of the efforts of contemporary economists as relatively sterile,2 and he has launched his own efforts to invigorate the discipline and make it more fruitful by the introduction of a new perspective, additional dimensions of economic analysis, and a new proposal for the objective of political economy. Over the years, Boulding has generated a profusion of publications which deal with a wide variety of topics.3 Yet, many of these efforts can be viewed as bits in an emerging mosaic of a broader conceptual context and framework for economics. Although Boulding's work has been widely published and acclaimed, it has not yet been given explicit attention as a system of thought. The purposes of this article are to bring together, in skeletal fashion, some of the major elements in Boulding's emerging system, to present them as components of a different "mega-perspective," and to suggest some possible implications for economics. These tasks are approached

Field of study: Economics
Integrative demographic modeling reveals population level impacts of PCB toxicity to juvenile snapping turtles.

A significant challenge in ecotoxicology and risk assessment lies in placing observed contaminant effects in a meaningful ecological context. Polychlorinated biphenyls (PCBs) have been shown to affect juvenile snapping turtle survival and growth but the ecological significance of these effects is difficult to discern without a formal, population-level assessment. We used a demographic matrix model to explore the potential population-level effects of PCBs on turtles. Our model showed that effects of PCBs on juvenile survival, growth and size at hatching could translate to negative effects at the population level despite the fact that these life cycle components do not typically contribute strongly to population level processes. This research points to the utility of using integrative demographic modeling approaches to better understand contaminant effects in wildlife. The results indicate that population-level effects are only evident after several years, suggesting that for long-lived species, detecting adverse contaminant effects could prove challenging.

Field of study: Environmental science
Serum suppressive activity of HIV seropositive patients.

The mechanisms by which HIV induces immunosuppression are still poorly understood so far. Several pathways of CD4 cell destruction are known, including cytolysis with or without syncitium formation and killing by cytotoxic effectors of HIV infected or non-infected CD4 cells. However, a discrepancy exists between the small number of actually infected cells in vivo and the extent of HIV-related immunodeficiency. Among other possible immunosuppressive factors, serum blocking factors have been reported, but only in AIDS-related opportunistic infections (OI), i.e. in a quite specific type of full-blown HIV disease. The purpose of this work was to determine whether serum blocking activity was unique to this group of patients, or if it was also expressed in other clinical presentations and, moreover, at earlier stages of the disease. We also attempted to delineate the nature of these seric factors. In order to do so, we assessed serum suppressive activity of 50 HIV seropositive patients, seven with OI, eight with Kaposi's sarcoma (KS), and 35 with no clinical AIDS. Our results confirm the existence of serum inhibiting factors in AIDS, and demonstrate their presence at earlier stages of the disease. They also highlight the fact that the level of serum suppression does not correlate with patients clinical status, but increases with the severity of the disease. The lower the CD4 count, the higher the suppression exerted. Furthermore, we showed that the suppression was at least partly mediated by small size molecules, which are not complement-mediated or directly lymphocytotoxic. On the other hand, this activity does not correlate with the serum level of p24 HIV core protein. The possible relation with other viral components is discussed. The relevance of these data to prognosis and pathogenesis of HIV disease deserves further investigation.

Field of study: Biology, Medicine
N,P-Codoped Carbon Layer Coupled with MoP Nanoparticles as an Efficient Electrocatalyst for Hydrogen Evolution Reaction

Efficient electrocatalyst plays a significant role on the development of hydrogen energy. In this work, an N,P-codoped carbon layer coupled with MoP nanoparticles (MoP/NPCs) was prepared through a facile high-temperature pyrolysis treatment. The obtained MoP/NPCs presented efficient activity for hydrogen evolution reaction (HER), with low onset potential of 90 mV, and a small Tafel slope (71 mV dec−1), as well as extraordinary stability in acidic electrolyte. This work provides a new facile strategy for the design and synthesis of sustainable and effective molybdenum-based electrocatalysts as alternatives to non-Pt catalysts for HER.

Field of study: Materials science
Microbiome Research Is Becoming the Key to Better Understanding Health and Nutrition

The human microbiome has emerged as the crucial moderator in the interactions between food and our body. It is increasingly recognised that the microbiome can change our mind and health status, or switch on a wide range of diseases including cancer, cardio-metabolic diseases, allergies, and obesity. The causes of diseases are often only partially understood. However, nutrients, metabolites, and microbes are increasingly regarded as key players, even where the complete disease mechanisms remain unclear. The key to progress in the future will be to use and exploit additional, newly emerging disciplines such as metagenomics to complement patient information and to bring our understanding of diseases and the interrelation and effects of nutritional molecules to the next level. The EU has already funded 216 projects under the 7th Framework Programme and Horizon 2020 programmes to promote metagenomics and to advance our knowledge of microbes. This support started with the catalysing MetaHIT project that has produced a catalogue of gut microbes, and has arrived now at the very multi-disciplinary SYSCID action looking at how the microbiome is driving its resilience potential and our health. Together, these projects involve an investment of more than €498 M. However, in Horizon 2020, the new EU Health and Food Work Programmes for 2018–2020 go even further by setting new goals to find applications and to generate more knowledge on the microbiome, nutrition, various hosts of microbes, and their relation to health and disease. The big vision is to modulate health and diseases via the microbiome and nutrition, while at the same time other factors such as omics, molecular signatures, and lifestyle are constant. In this way, microbiome and nutrition research is moving from an isolated and despised offside position to a beacon of hope with a lot of potential and possibilities.

Field of study: Biology