bluuebunny/crossref_metadata_2025_split huggingface dataset:
A protocol for the annotation of evaluative stance and metaphor across four discourse genres
Authors: Hidalgo-Downing Laura , Pérez-Sobrino Paula , Filardo-Llamas Laura , Maíz-Arévalo Carmen , Núñez-Perucha Begoña , Sánchez-Moya Alfonso , Williams Camus Julia T. 
Published: March 2024

Abstract
The present article contributes to research on evaluation by addressing two complementary objectives: first, we
present a protocol for the identification and annotation of evaluation in English discourse and, second, we show the results of
the implementation of the protocol in the annotation of evaluation in a sample of a corpus of four genres. We first describe the
protocol by discussing the theoretical and methodological grounding of the annotation scheme, the criteria, the categories, the
steps for the implementation of the protocol and an illustrative example of the application of the protocol to a short extract. We
subsequently provide the preliminary results of a pilot study with the frequency of evaluative expressions across the four genres.
Results show that while adjectives and non-metaphoric evaluative expressions are overall more frequent, there are differences
regarding the preference for positive or negative value and regarding the frequency of function.
Physical insights into trapping effects on vertical GaN-on-Si trench MOSFETs from TCAD
Authors: Zagni Nicolò , Fregolent Manuel , Fiol Andrea Del , Favero Davide , Bergamin Francesco , Verzellesi Giovanni , Santi Carlo De , Meneghesso Gaudenzio , Zanoni Enrico , Huber Christian , Meneghini Matteo , Pavan Paolo 
Published: March 2024

Abstract
Vertical GaN power MOSFET is a novel technology that offers great potential for power switching applications. Being still in an early development phase, vertical GaN devices are yet to be fully optimized and require careful studies to foster their development. In this work, we report on the physical insights into device performance improvements obtained during the development of vertical GaN-on-Si trench MOSFETs (TMOS’s) provided by TCAD simulations, enhancing the dependability of the adopted process optimization approaches. Specifically, two different TMOS devices are compared in terms of transfer-curve hysteresis (H) and subthreshold slope (SS), showing a ≈ 75% H reduction along with a ≈ 30% SS decrease. Simulations allow attributing the achieved improvements to a decrease in the border and interface traps, respectively. A sensitivity analysis is also carried out, allowing to quantify the additional trap density reduction required to minimize both figures of merit.
Behavior of exciton in direct−indirect band gap Al
x
Ga1−x
As crystal lattice quantum wells
Authors: Sun Yong , Zhang Wei , Han Shuang , An Ran , Tang Xin-Sheng , Yu Xin-Lei , Miao Xiu-Juan , Ma Xin-Jun , Xianglian  , Li Pei-Fang , Zhao Cui-Lan , Ding Zhao-Hua , Xiao Jing-Lin 
Published: March 2024

Abstract
Excitons have significant impacts on the properties of semiconductors. They exhibit significantly different properties when a direct semiconductor turns in to an indirect one by doping. Huybrecht variational method is also found to influence the study of exciton ground state energy and ground state binding energy in Al
x
Ga1−x
As semiconductor spherical quantum dots. The Al
x
Ga1−x
As is considered to be a direct semiconductor at Al concentration below 0.45, and an indirect one at the concentration above 0.45. With regards to the former, the ground state binding energy increases and decreases with Al concentration and eigenfrequency, respectively; however, while the ground state energy increases with Al concentration, it is marginally influenced by eigenfrequency. On the other hand, considering the latter, while the ground state binding energy increases with Al concentration, it decreases with eigenfrequency; nevertheless, the ground state energy increases both with Al concentration and eigenfrequency. Hence, for the better practical performance of the semiconductors, the properties of the excitons are suggested to vary by adjusting Al concentration and eigenfrequency
Design and commissioning of a Silicon Photomultiplier-based dosimeter for Low Dose Rate (LDR) oncological brachytherapy
Authors: Burdyko A. , Caccia M. , Giaz A. , Santoro R. , Tomaciello G. 
Published: March 2024

Abstract
Brachytherapy is a radiotherapy procedure performed with radioactive sources implanted into the patient's body, close to the area affected by cancer. This is a reference procedure for the treatment of prostate and gynecologic cancer due to the reduction of the dose released close to organs at risk (e.g., rectum, bladder, colon). For this reason, real-time dose verification and source localisation are essential for an optimal treatment plan. The ORIGIN collaboration aims to achieve this goal through a 16-fibre sensor system, designed
to house a small volume of scintillating material in a transparent fibre tip to enable point-like measurements.
The selected scintillating materials feature a decay time of about 500 μs and the signal associated with the primary γ-ray interaction results in the emission of a sequence of single photons distributed over time. Therefore, the dosimeter requires a detector with single-photon sensitivity and a system designed to provide dose measurements by photon counting.
Uniformity of fibre response, system stability and reproducibility of measurements are key features of the dosimeter. The characterisation of the 16-channel dosimeter system equipped with thermo-electrically cooled Silicon Photomultipliers, carried out in the laboratory using an X-ray cabinet, is discussed and the results are compared with an earlier version equipped with SiPMs operated at room temperature.
Low-energy ion beam diagnostics: an integrated solution
Authors: Adıgüzel A. , Çetinkaya H. , Esen Ş. , Halis D. , İlhan T.B. , Kılıçgedik A. , Oğur S. , Öz S. , Özbey A. , Özcan V.E. , Ünel N.G. 
Published: March 2024

Abstract
High gradient accelerator injectors have been widely studied
throughout the world-leading accelerator facilities. The demand for
high frequency cavities has led the Detector, Accelerator and
instrumentation laboratory (KAHVELab) in Istanbul to deploy a
four-vane Radio Frequency Quadrupole (RFQ) operating at 800 MHz to
accelerate 20 keV protons to 2 MeV. The protons from the
microwave discharge ion source are transversely matched to the RFQ
via an optimized Low Energy Beam Transport (LEBT) line which also
contains an integrated measurement station, called measurement
station (MBOX). The MBOX is used to measure the proton beam's
current along with pulse length duration, profile as well as the
beam emittance upstream of the RFQ. It contains a number of
home-built diagnostic tools: a Faraday cup, a scintillator screen
and a pepper pot plate (PP). The analysis software is also locally
developed and tested for the PP photo analysis. In this note, the
design, construction and tests of the integrated measurement station
are discussed. The results from various measurements, especially on
beam profile and charge, are compared to the simulation
predictions.
Nuclear deformation and cell division of single cell on elongated micropatterned substrates fabricated by DMD lithography
Authors: Zhang Duo , Wu Wenjie , Zhang Wanying , Feng Qiyu , Zhang Qingchuan , Liang Haiyi 
Published: March 2024

Abstract
Cells sense mechanical signals from the surrounding environment and transmit them to the nucleus through mechanotransduction to regulate cellular behavior. Microcontact printing, which utilizes elastomer stamps, is an effective method for simulating the cellular microenvironment and manipulating cell morphology. However, the conventional fabrication process of silicon masters and elastomer stamps requires complex procedures and specialized equipment, which restricts the widespread application of micropatterning in cell biology and hinders the investigation of the role of cell geometry in regulating cell behavior. In this study, we present an innovative method for convenient resin stamp microfabrication based on digital micromirror device planar lithography. Using this method, we generated a series of patterns ranging from millimeter to micrometer scales and validated their effectiveness in controlling adhesion at both collective and individual cell levels. Additionally, we investigated mechanotransduction and cell behavior on elongated micropatterned substrates. We then examined the effects of cell elongation on cytoskeleton organization, nuclear deformation, focal adhesion formation, traction force generation, nuclear mechanics, and the growth of HeLa cells. Our findings reveal a positive correlation between cell length and mechanotransduction. Interestingly, HeLa cells with moderate length exhibit the highest cell division and proliferation rates. These results highlight the regulatory role of cell elongation in mechanotransduction and its significant impact on cancer cell growth. Furthermore, our methodology for controlling cell adhesion holds the potential for addressing fundamental questions in both cell biology and biomedical engineering.
Analyzing clinical laboratory specimen rejection rates at a specialized hospital in Ethiopia: A 2-year document review
Authors: Deress Teshiwal , Abebaw Yeshewas , Esayas Yezena , Nebertu Semegn , Kinidie Meseret , Abebe Germaw , Bayleyegn Biruk 
Published: March 2024

Abstract

Objectives
Accurate laboratory diagnosis is essential for effective patient care, but the rejection of specimens within laboratories can have serious consequences.

Methods
A retrospective cross-sectional study was conducted from September to November 2021 at the University of Gondar Comprehensive Specialized Hospital laboratory. Two years of laboratory data were collected from laboratory log books and analyzed to determine trends in specimen rejection rates and identify potential reasons for those rejections.

Results
We analyzed 114,439 specimens, of which 786 (0.70%) were rejected. The hematology service exhibited the highest rejection rate, at 273 (0.2%). The main reasons for specimen rejection were specimens without requests or requests without specimens (40.2%), poor smear preparation (12.3%), clotted specimens (11.3%), and labeling problems (8.0%).

Conclusions
This study emphasized a significant incidence of specimen rejection, particularly in the hematology laboratory, underscoring the need for immediate implementation of corrective actions and preventive measures. Furthermore, conducting comprehensive larger-scale studies is recommended to deepen our understanding of and investigate the specific factors contributing to specimen rejection in greater detail.
Niche and phenotypic differentiation in fern hybrid speciation, a case study of Pteris fauriei (Pteridaceae)
Authors: Chao Yi-Shan , Yang Yao-Wei , Sheue Chiou-Rong , Lai I-Ling 
Published: March 2024

Abstract

Background and Aims
Niche differentiation is a crucial issue in speciation. Although it has a well-known role in adaptive processes of hybrid angiosperms, it is less understood in hybrid ferns. Here, we investigate whether an intermediate ecological niche of a fern hybrid is a novel adaptation that provides insights into fern hybrid speciation.

Methods
Pteris fauriei (Pteridaceae) is a natural hybrid fern, occurring in environments between its parent species. The maternal Pteris minor is found in sunny areas, but the habitat of the paternal Pteris latipinna is shady. We combined data from morphology, leaf anatomy and photosynthetic traits to explore adaptation and differentiation, along with measuring the environmental features of their niches. We also performed experiments in a common garden to understand ecological plasticity.

Key Results
The hybrid P. fauriei was intermediate between the parent species in stomatal density, leaf anatomical features and photosynthetic characteristics in both natural habitats and a common garden. Interestingly, the maternal P. minor showed significant environmental plasticity and was more similar to the hybrid P. fauriei in the common garden, suggesting that the maternal species experiences stress in its natural habitats but thrives in environments similar to those of the hybrid.

Conclusions
Based on the similar niche preferences of the hybrid and parents, we propose hybrid superiority. Our results indicate that the hybrid P. fauriei exhibits greater fitness and can compete with and occupy the initial niches of the maternal P. minor. Consequently, we suggest that the maternal P. minor has experienced a niche shift, elucidating the pattern of niche differentiation in this hybrid group. These findings offer a potential explanation for the frequent occurrence of hybridization in ferns and provide new insights into fern hybrid speciation, enhancing our understanding of fern diversity.
A 7-Year Retrospective Analysis of Hymenoplasty: Profiles From a Specialized Gynecological Cosmetic Surgery Practice
Authors: Konaç Ayşe 
Published: March 2024

Abstract

Background
Hymenoplasty—surgical reconstruction of the hymen—is on the rise in Turkey, reflecting the enduring importance of virginity which is rooted in sociocultural and religious beliefs. Demographic factors shape women's decisions regarding this procedure.

Objectives
The aim of this investigation was to delve into the multifaceted perceptions around virginity and hymenoplasty in Turkey, examining the impact of sociocultural and religious beliefs on women's decisions. The study also explored demographic influences, offering insights into the societal and cultural backdrop of hymenoplasty.

Methods
A 7-year retrospective analysis of 4259 patient records (2015-2022) at a private clinic was conducted, and statistical tools were used to meticulously analyze data on demographics and shared decision-making dynamics.

Results
In the examined cohort (83.3%), the choice of permanent hymenoplasty was prevalent among individuals aged 14 to 49 years, with 58.6% being engaged and seeking the procedure a week before marriage. Notably, 91.0% were accompanied by friends during consultations, and a minority disclosed a history of childbirth or experience of forced intercourse. An increasing trend in first-time and post-assault hymenoplasty procedures was observed in 2021. Geographically, the majority of individuals resided in Istanbul, but represented all Turkish regions. Additional procedures such as vaginoplasty were common, with mostly successful postprocedural outcomes and minor complications.

Conclusions
This study highlighted the enduring social importance of virginity in Turkey, emphasizing hymenoplasty as a coping strategy for psychological and societal challenges. The study calls for comprehensive patient support and societal progress in respecting women's bodily autonomy, urging a shift away from the cultural fixation on virginity.

Level of Evidence: 4
Mapping drug biology to disease genetics to discover drug impacts on the human phenome
Authors: Habib Mamoon , Lalagkas Panagiotis Nikolaos , Melamed Rachel D 
Published: March 2024

Abstract

Motivation
Medications can have unexpected effects on disease, including not only harmful drug side effects, but also beneficial drug repurposing. These effects on disease may result from hidden influences of drugs on disease gene networks. Then, discovering how biological effects of drugs relate to disease biology can both provide insight into the mechanism of latent drug effects, and can help predict new effects.

Results
Here, we develop Draphnet, a model that integrates molecular data on 429 drugs and gene associations of nearly 200 common phenotypes to learn a network that explains drug effects on disease in terms of these molecular signals. We present evidence that our method can both predict drug effects, and can provide insight into the biology of unexpected drug effects on disease. Using Draphnet to map a drug’s known molecular effects to downstream effects on the disease genome, we put forward disease genes impacted by drugs, and we suggest a new grouping of drugs based on shared effects on the disease genome. Our approach has multiple applications, including predicting drug uses and learning drug biology, with implications for personalized medicine.

Availability and implementation
Code to reproduce the analysis is available at https://github.com/RDMelamed/drug-phenome
Development of a CT-based radiomics-clinical model to diagnose acute pancreatitis on nonobvious findings on CT in children with pancreaticobiliary maljunction
Authors: Cai Tian-na , Zhao Lian , Yang Yang , Mao Hui-min , Huang Shun-gen , Guo Wan-liang 
Published: March 2024

Abstract

Objectives
Since neither abdominal pain nor pancreatic enzyme elevation is specific for acute pancreatitis (AP), the diagnosis of AP in patients with pancreaticobiliary maljunction (PBM) may be challenging when the pancreas appears normal or nonobvious on CT. This study aimed to develop a quantitative radiomics-based nomogram of pancreatic CT for identifying AP in children with PBM who have nonobvious findings on CT.

Methods
PBM patients with a diagnosis of AP evaluated at the Children’s Hospital of Soochow University from June 2015 to October 2022 were retrospectively reviewed. The radiological features and clinical factors associated with AP were evaluated. Based on the selected variables, multivariate logistic regression was used to construct clinical, radiomics, and combined models.

Results
Two clinical parameters and 6 radiomics characteristics were chosen based on their significant association with AP, as demonstrated in the training (area under curve [AUC]: 0.767, 0.892) and validation (AUC: 0.757, 0.836) datasets. The radiomics-clinical nomogram demonstrated superior performance in both the training (AUC, 0.938) and validation (AUC, 0.864) datasets, exhibiting satisfactory calibration (P &gt; .05).

Conclusions
Our radiomics-based nomogram is an accurate, noninvasive diagnostic technique that can identify AP in children with PBM even when CT presentation is not obvious.

Advances in knowledge
This study extracted imaging features of nonobvious pancreatitis. Then it developed and evaluated a combined model with these features.
Fused heteroaromatic donor–acceptor fluorophores: enhanced brightness and variable emission characteristics
Authors: Sumida Ayaka , Takahashi Shohei , Nagai Sayaka , Ito Suguru 
Published: March 2024

Abstract
Octacyclic imidazophenanthridine derivatives have been synthesized by the intramolecular C–H arylation of phenanthroimidazolylbenzothiadiazoles. A significant increase in the molar extinction coefficient (ε) compared with their non-fused counterparts has been achieved, while retaining the high fluorescence quantum yield (ΦF). Their luminescence properties vary in various solvents, as well as in crystalline and mechanically ground states.
A Validated Highly Sensitive Microsatellite Instability Assay Accurately Identifies Individuals Harboring Biallelic Germline PMS2 Pathogenic Variants in Constitutional Mismatch Repair Deficiency
Authors: Marín Fátima , Canet-Hermida Júlia , Bianchi Vanessa , Chung Jiil , Wimmer Katharina , Foulkes William , Pérez-Alonso Vanesa , Domínguez-Pinilla Nerea , Sábado Constantino , Vázquez-Gómez Felisa , Molinés Antonio , Fioravantti Victoria , Carrasco Estela , Stengs Lucie , Edwards Melissa , Negm Logine , Das Anirban , Aronson Melyssa , Pastor Ángela , Rueda Daniel , González-Granado Luis Ignacio , Tabori Uri , Capellá Gabriel , Pineda Marta 
Published: March 2024

Abstract

Background
Constitutional mismatch repair deficiency (CMMRD) is a rare and extraordinarily penetrant childhood-onset cancer predisposition syndrome. Genetic diagnosis is often hampered by the identification of mismatch repair (MMR) variants of unknown significance and difficulties in PMS2 analysis, the most frequently mutated gene in CMMRD. We present the validation of a robust functional tool for CMMRD diagnosis and the characterization of microsatellite instability (MSI) patterns in blood and tumors.

Methods
The highly sensitive assessment of MSI (hs-MSI) was tested on a blinded cohort of 66 blood samples and 24 CMMRD tumor samples. Hs-MSI scores were compared with low-pass genomic instability scores (LOGIC/MMRDness). The correlation of hs-MSI scores in blood with age of cancer onset and the distribution of insertion-deletion (indel) variants in microsatellites were analyzed in a series of 169 individuals (n = 68 CMMRD, n = 124 non-CMMRD).

Results
Hs-MSI achieved high accuracy in the identification of CMMRD in blood (sensitivity 98.5% and specificity 100%) and detected MSI in CMMRD-associated tumors. Hs-MSI had a strong positive correlation with whole low-pass genomic instability LOGIC scores (r = 0.89, P = 2.2e-15 in blood and r = 0.82, P = 7e-3 in tumors). Indel distribution identified PMS2 pathogenic variant (PV) carriers from other biallelic MMR gene PV carriers with an accuracy of 0.997. Higher hs-MSI scores correlated with younger age at diagnosis of the first tumor (r = −0.43, P = 0.011).

Conclusions
Our study confirms the accuracy of the hs-MSI assay as ancillary testing for CMMRD diagnosis, which can also characterize MSI patterns in CMMRD-associated cancers. Hs-MSI is a powerful tool to pinpoint PMS2 as the affected germline gene and thus potentially personalize cancer risk.
Intra-tooth stable isotope analysis reveals seasonal dietary variability and niche partitioning among bushpigs/red river hogs and warthogs
Authors: Yang Deming , Uno Kevin T , Cerling Thure E , Mwebi Ogeto , Leakey Louise N , Grine Frederick E , Souron Antoine 
Published: March 2024

Abstract
How animals respond to seasonal resource availability has profound implications for their dietary flexibility and realized ecological niches. We sought to understand seasonal dietary niche partitioning in extant African suids using intra-tooth stable isotope analysis of enamel. We collected enamel samples from canines of red river hogs/bushpigs (Potamochoerus spp.) and third molars of warthogs (Phacochoerus spp.) in 3 different regions of central and eastern Africa. We analyzed multiple samples from each tooth and used variations in stable carbon and oxygen isotope ratios (δ13C and δ18O) and covariances between them to infer seasonal dietary changes. We found that most Phacochoerus display C4-dominated diets, while most Potamochoerus display C3-dominated diets. Phacochoerus and Potamochoerus that co-occur in the same region display no overlap in intra-tooth δ13C, which suggests dietary niche partitioning. They also show diverging δ13C values as the dry seasons progress and converging δ13C values during the peak of the rainy seasons, which suggests a greater dietary niche separation during the dry seasons when resources are scarce than during the rainy season. We found statistically significant cross-correlations between intra-tooth δ13C and δ18O in most specimens. We also observed a temporal lag between δ13C and δ18O in some specimens. This study demonstrates that intra-tooth stable isotope analysis is a promising approach to investigate seasonal dietary niche variation. However, large inter-individual variations in δ18O at certain localities can be challenging to interpret. Future studies that expand the intra-tooth stable isotope surveys or include controlled feeding experiments will improve its application in ecological studies.