bluuebunny/crossref_metadata_2025_split huggingface dataset:
ReqNet and ReqSim: A Network and Semantic Similarity Dataset of Requirements from the Tree Structure of System Requirement Specifications
Authors: Sahu Chandan Kumar , Rai Rahul , Wiecek Margaret , Gorsich David 
Published: June 2024

Abstract
Systems are developed as a solution to the problem space defined by their requirements. The requirements are acquired during the elicitation process. The creative nature of the elicitation process, proprietary nature of requirements, the need of extensive preprocessing and the diverse techniques for analysis restricts the development of a requirement dataset. There exists no standard method to create a requirement dataset. Thus, we devise a semi-formal method to create a multi-purpose requirement dataset that harnesses human knowledge in the system requirement specification documents (SyRSDs) to facilitate the deployment of modern computing algorithms. Our dataset has three forms. (1) ReqList, a list of requirements from 86 distinct systems with their document structure in pure text form. The 12701 requirements are ready to leverage natural language processing techniques and unsupervised machine learning techniques. (2) ReqNet, a large network of requirements consisting of 17375 nodes to deploy graph-theoretic algorithms for requirement engineering. ReqNet portrays small-world network characteristics with an average distance of 9.5619 links. (3) ReqSim, a dataset consisting of 10933 pairs of requirements annotated with their similarity scores. ReqSim enables sentence-level supervised learning tasks to exploit the semantics of requirements. The similarity scores are coherent with human knowledge. Our dataset is grounded by the tree structure of SyRSDs. We devise a method to extract a tree from the SyRSDs. The tree structure resonates with the hierarchical nature of the requirement allocation process. The ReqList, ReqNet and ReqSim dataset is available at https://github.com/ChandanKSahu/ReqList_ReqNet_ReqSim.
A Microchannel Heat Exchanger Produced From a Metal Matrix Composite by Hybrid Laser Powder Bed Fusion and Inkjet Printing
Authors: Lee Kijoon , Ghayoor Milad , Doddapaneni V. Vinay K. , Noma Kenta , Pasebani Somayeh , Chang Chih-Hung , Fronk Brian , Paul Brian K. 
Published: June 2024

Abstract
This paper explores the production of an oxide dispersion strengthened (ODS) 304L stainless steel microchannel heat exchanger (HX) using a hybrid additive manufacturing process of laser powder bed fusion and inkjet printing. The study investigates the capabilities and economics of the hybrid inkjet-laser powder bed fusion (LPBF) process and evaluates the dimensional accuracy, functionality, and mechanical properties of the resulting ODS alloy. The effectiveness and pressure drop of the ODS heat exchangers produced by the hybrid LPBF tool are also determined. Results show that the inkjet-doped samples have a lower mean channel height with higher standard deviation than samples produced by LPBF alone. This is attributed to greater absorption of laser energy for the powder coated with the oxide precursor. The economic analysis shows that the hybrid process has a potential for reducing the unit cost of the heat exchanger based on cost modeling assumptions.
Synchronous Comparison of Two Thulium Optical Clocks
Authors: Golovizin A. , Mishin D. , Provorchenko D. , Tregubov D. , Kolachevsky N. 
Published: June 2024

The experimental comparison of two thulium optical lattice clocks in a time interval of up to one hour has been carried out. The synchronous comparison of a clock transition in two independent atomic ensembles using a single ultrastable laser has allowed us to eliminate fluctuations of the laser frequency from the measured frequency difference and to reach a relative measurement error of 10–16 after 500-s averaging, which corresponds to a relative instability of $$2 \times {{10}^{{ - 15}}}{\text{/}}\sqrt \tau $$. The successful demonstration of the long-term operation of two systems using the synchronous comparison of clock transitions opens the possibility of studying systematic shifts in thulium optical clocks with an uncertainty of 10–17.
Detecting Small Cell Transformation in Patients with Advanced EGFR Mutant Lung Adenocarcinoma through Epigenomic cfDNA Profiling
Authors: El Zarif Talal , Meador Catherine B. , Qiu Xintao , Seo Ji-Heui , Davidsohn Matthew P. , Savignano Hunter , Lakshminarayanan Gitanjali , McClure Heather M. , Canniff John , Fortunato Brad , Li Rong , Banwait Mandeep K. , Semaan Karl , Eid Marc , Long Henry , Hung Yin P. , Mahadevan Navin R. , Barbie David A. , Oser Matthew G. , Piotrowska Zofia , Choueiri Toni K. , Baca Sylvan C. , Hata Aaron N. , Freedman Matthew L. , Berchuck Jacob E. 
Published: June 2024

Abstract

Purpose:
Histologic transformation to small cell lung cancer (SCLC) is a mechanism of treatment resistance in patients with advanced oncogene-driven lung adenocarcinoma (LUAD) that currently requires histologic review for diagnosis. Herein, we sought to develop an epigenomic cell-free DNA (cfDNA)-based approach to noninvasively detect small cell transformation in patients with EGFR mutant (EGFRm) LUAD.

Experimental Design:
To characterize the epigenomic landscape of transformed (t)SCLC relative to LUAD and de novo SCLC, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to profile the histone modifications H3K27ac, H3K4me3, and H3K27me3; methylated DNA immunoprecipitation sequencing (MeDIP-seq); assay for transposase-accessible chromatin sequencing; and RNA sequencing on 26 lung cancer patient-derived xenograft (PDX) tumors. We then generated and analyzed H3K27ac ChIP-seq, MeDIP-seq, and whole genome sequencing cfDNA data from 1 mL aliquots of plasma from patients with EGFRm LUAD with or without tSCLC.

Results:
Analysis of 126 epigenomic libraries from the lung cancer PDXs revealed widespread epigenomic reprogramming between LUAD and tSCLC, with a large number of differential H3K27ac (n = 24,424), DNA methylation (n = 3,298), and chromatin accessibility (n = 16,352) sites between the two histologies. Tumor-informed analysis of each of these three epigenomic features in cfDNA resulted in accurate noninvasive discrimination between patients with EGFRm LUAD versus tSCLC [area under the receiver operating characteristic curve (AUROC) = 0.82–0.87]. A multianalyte cfDNA-based classifier integrating these three epigenomic features discriminated between EGFRm LUAD versus tSCLC with an AUROC of 0.94.

Conclusions:
These data demonstrate the feasibility of detecting small cell transformation in patients with EGFRm LUAD through epigenomic cfDNA profiling of 1 mL of patient plasma.
Heterogeneous Thresholds, Social Ranking, and the Emergence of Vague Categories
Authors: Lawry Jonathan 
Published: June 2024

Abstract
Threshold models in which an individual’s response to a particular state of the world depends on whether an associated measured value exceeds a given threshold are common in a variety of social learning and collective decision-making scenarios in both natural and artificial systems. If thresholds are heterogeneous across a population of agents, then graded population level responses can emerge in a context in which individual responses are discrete and limited. In this article, I propose a threshold-based model for social learning of shared quality categories. This is then combined with the voting model of fuzzy categories to allow individuals to learn membership functions from their peers, which can then be used for decision-making, including ranking a set of available options. I use agent-based simulation experiments to investigate variants of this model and compare them to an individual learning benchmark when applied to the ranking problem. These results show that a threshold-based approach combined with category-based voting across a social network provides an effective social mechanism for ranking that exploits emergent vagueness.
Outsourcing Control Requires Control Complexity
Authors: Langer Carlotta , Ay Nihat 
Published: June 2024

Abstract
An embodied agent influences its environment and is influenced by it. We use the sensorimotor loop to model these interactions and quantify the information flows in the system by information-theoretic measures. This includes a measure for the interaction among the agent’s body and its environment, often referred to as morphological computation. Additionally, we examine the controller complexity, which can be seen in the context of the integrated information theory of consciousness. Applying this framework to an experimental setting with simulated agents allows us to analyze the interaction between an agent and its environment, as well as the complexity of its controller. Previous research revealed that a morphology adapted well to a task can substantially reduce the required complexity of the controller. In this work, we observe that the agents first have to understand the relevant dynamics of the environment to interact well with their surroundings. Hence an increased controller complexity can facilitate a better interaction between an agent’s body and its environment.
Impact of soil moisture regimes on greenhouse gas emissions, soil microbial biomass, and enzymatic activity in long-term fertilized paddy soil
Authors: Shah Asad , Huang Jing , Han Tianfu , Khan Muhammad Numan , Tadesse Kiya Adare , Daba Nano Alemu , Khan Sajeela , Ullah Sami , Sardar Muhammad Fahad , Fahad Shah , Zhang Huimin 
Published: June 2024

AbstractTwo potent greenhouse gases that are mostly found in agricultural soils are methane and nitrous oxide. Therefore, we investigated the effect of different moisture regimes on microbial stoichiometry, enzymatic activity, and greenhouse gas emissions in long-term paddy soils. The treatments included a control (CK; no addition), chemical fertilizer (NPK), and NPK + cattle manure (NPKM) and two moisture regimes such as 60% water-filled pore spaces (WFPS) and flooding. The results revealed that 60% water-filled pore spaces (WFPS) emit higher amounts of N2O than flooded soil, while in the case of CH4 the flooded soil emits more CH4 emission compared to 60% WFPS. At 60% WFPS higher N2O flux values were recorded for control, NPK, and NPKM which are 2.3, 3.1, and 3.5 µg kg−1, respectively. In flooded soil, the CH4 flux emission was higher, and the NPKM treatment recorded the maximum CH4 emissions (3.8 µg kg−1) followed by NPK (3.2 µg kg−1) and CK (1.7 µg kg−1). The dissolved organic carbon (DOC) was increased by 15–27% under all flooded treatments as compared to 60% WPFS treatments. The microbial biomass carbon, nitrogen, and phosphorus (MBC, MBN, and MBP) significantly increased in the flooded treatments by 8–12%, 14–21%, and 4–22%, respectively when compared to 60% WFPS. The urease enzyme was influenced by moisture conditions, and significantly increased by 42–54% in flooded soil compared with 60% WFPS while having little effect on the β-glucosidase (BG) and acid phosphatase (AcP) enzymes. Moreover DOC, MBC, and pH showed a significant positive relationship with cumulative CH4, while DOC showed a significant relationship with cumulative N2O. In the random forest model, soil moisture, MBC, DOC, pH, and enzymatic activities were the most important factors for GHG emissions. The PLS-PM analysis showed that soil properties and enzymes possessed significantly directly impacted on CH4 and N2O emissions, while SMB had indirect positive effect on CH4 and N2O emissions.
Genome-wide association study, combined with bulk segregant analysis, identify plant receptors and defense related genes as candidate genes for downy mildew resistance in quinoa
Authors: Fondevilla Sara , Calderón-González Álvaro , Rojas-Panadero Borja , Cruz Verónica , Matías Javier 
Published: June 2024

Abstract
Background
Downy mildew is the most relevant disease of quinoa and the most widespread. Though, little is known about the genetics of resistance to this disease. The objective of this study was to identify the genomic regions controlling downy mildew resistance in quinoa and candidate genes for this trait. With this aim we carried out a GWAS analysis in a collection formed by 211 quinoa accessions from different origins. This approach was combined with inheritance studies and Bulk Segregant Analysis (BSA) in a segregating population.

Results
GWAS analysis identified 26 genomic regions associated with the trait. Inheritance studies in a F2 population segregating for resistance revealed the existence of a major single dominant gene controlling downy mildew complete resistance in quinoa accession PI614911. Through BSA, this gene was found to be located in chromosome 4, in a region also identified by GWAS. Furthermore, several plant receptors and resistance genes were found to be located into the genomic regions identified by GWAS and are postulated as candidate genes for resistance.

Conclusions
Until now, little was known about the genetic control of downy mildew resistance in quinoa. A previous inheritance study suggested that resistance to this disease was a quantitative polygenic trait and previous GWAS analyses were unable to identify accurate markers for this disease. In our study we demonstrate the existence of, at least, one major gene conferring resistance to this disease, identify the genomic regions involved in the trait and provide plausible candidate genes involved in defense. Therefore, this study significantly increases our knowledge about the genetics of downy mildew resistance and provides relevant information for breeding for this important trait.
Lidocaine spray vs mepivacaine local infiltration for suturing 1st/2nd grade perineal lacerations: a randomised controlled non-inferiority trial
Authors: Restaino Stefano , Degano Matilde , Rizzante Elisa , Battello Ginevra , Paparcura Federico , Biasioli Anna , Arcieri Martina , Filip Gabriele , Vetrugno Luigi , Dogareschi Teresa , Bove Tiziana , Petrillo Marco , Capobianco Giampiero , Vizzielli Giuseppe , Driul Lorenza ,   LISPRAY Group, Moroni Rossana , Zanin Valentina , Tius Veronica , Celante Lisa , Sala Alessia , Poli Alice , Pregnolato Sara , Seminara Giuseppina , Cuman Margherita , Pellecchia Giulia , Occhiali Tommaso , Giorgiutti Cristina , Liviero Stefania , Mazzera Ilaria , Padovani Diana , De Gennaro Elena 
Published: June 2024

Abstract
Background
Perineal lacerations are a very common complication of post-partum. Usually, the repair of 1st and 2nd-grade lacerations is performed after the administration of local anesthesia. Despite the great relevance of the problem, there are only a few studies about the best choice of local anesthetic to use during suturing. We performed a randomised controlled trial to evaluate the efficacy and safety of the use of a local anesthetic spray during the suturing of perineal lacerations in the post-partum.

Methods
We compared the spray with the standard technique, which involves the infiltration of lacerated tissues, using the NRS scale. 136 eligible women who had given birth at University Hospital of Udine were enrolled and randomly assigned to receive nebulization of Lidocaine hydrochloride 10% spray (experimental group) or subcutaneous/submucosal infiltration of mepivacaine hydrochloride (control group) during suturing of perineal laceration.

Results
The lacerations included 84 1st-grade perineal traumas (61.7%) and 52 2nd-grade perineal traumas (38.2%). All the procedures were successfully completed without severe complications or serious adverse reactions. There were no statistically significant differences between the two groups in terms of blood losses or total procedure time. Moreover, there were no statistically significant differences in terms of NRS to none of the intervals considered. Regarding the application of the spray in the B group, in 36 cases (52.9%) it was necessary to improve the number of puffs previously supposed to be sufficient (5 puffs). Just in 3 cases, an additional injection was necessary (4.4%).

Conclusions
Our study demonstrates that lidocaine spray alone can be used as a first line of local anesthetic during the closure of I-II-grade perineal lacerations, as it has comparable efficacy to mepivacaine infiltration.

Trial registration
The trial was recorded on https://clinicaltrials.gov. Identification number: NCT05201313. First registration date: 21/01/2022. Unique Protocol ID: 0042698/P/GEN/ARCS.
Constructing a prognostic model for colon cancer: insights from immunity-related genes
Authors: Li Ansu , Li Qi , Wang Chaoshan , Bao Xue , Sun Feng , Qian Xiaoping , Sun Wu 
Published: June 2024

Abstract
Background
Colon cancer (CC) is a malignancy associated with significant morbidity and mortality within the gastrointestinal tract. Recurrence and metastasis are the main factors affecting the prognosis of CC patients undergoing radical surgery; consequently, we attempted to determine the impact of immunity-related genes.

Result
We constructed a CC risk model based on ZG16, MPC1, RBM47, SMOX, CPM and DNASE1L3. Consistently, we found that a significant association was found between the expression of most characteristic genes and tumor mutation burden (TMB), microsatellite instability (MSI) and neoantigen (NEO). Additionally, a notable decrease in RBM47 expression was observed in CC tissues compared with that in normal tissues. Moreover, RBM47 expression was correlated with clinicopathological characteristics and improved disease-free survival (DFS) and overall survival (OS) among patients with CC. Lastly, immunohistochemistry and co-immunofluorescence staining revealed a clear positive correlation between RBM47 and CXCL13 in mature tertiary lymphoid structures (TLS) region.

Conclusion
We conclude that RBM47 was identified as a prognostic-related gene, which was of great significance to the prognosis evaluation of patients with CC and was correlated with CXCL13 in the TLS region.
Analysis of clinical characteristics of different types of lung function impaiement in TDL patients
Authors: Zhao Jing , Cao Xiaoman , Li YunSong , Li Yang , Ma Teng , Liu Fangchao , Ruan Hongyun 
Published: June 2024

Abstract
Aim
The clinical characteristics associated with pulmonary function decline in patients with Tuberculosis-destroyed lung (TDL) remain uncertain. We categorize them based on the pattern of pulmonary function impairment, distinguishing between restrictive spirometric pattern (RSP) and obstructive spirometric pattern (OSP). We aim to compare the severity of these patterns with the clinical characteristics of TDL patients and analyze their correlation.

Method
We conducted a retrospective analysis on the clinical data of TDL patients who underwent consecutive pulmonary function tests (PFT) from November 2002 to February 2023. We used the lower limit formula for normal values based on the 2012 Global Lung Function Initiative. We compared the clinical characteristics of RSP patients with those of OSP patients. The characteristics of RSP patients were analyzed using the tertiles of forced vital capacity percentage predicted (FVC% pred) decline based on PFT measurements, and the characteristics of OSP patients were analyzed using the tertiles of forced expiratory volume in 1 s percentage predicted (FEV1% pred) decline.

Result
Among the RSP patients, those in the Tertile1 group (with lower FVC% pred) were more likely to have a higher of body mass index (BMI), spinal deformities, and C-reactive protein (CRP) compared to the other two groups (P for trend < 0.001, 0.027, and 0.013, respectively). Among OSP patients, those in the Tertile1 group (with lower FEV1% pred) showed an increasing trend in cough symptoms and contralateral lung infection compared to the Tertile 2–3 group (P for trend 0.036 and 0.009, respectively).

Conclusion
For TDL patients, we observed that Patients with high BMI, a higher proportion of spinal scoliosis, and abnormal elevation of CRP levels were more likely to have reduced FVC. Patients with decreased FEV1% pred have more frequent cough symptoms and a higher proportion of lung infections on the affected side.
Physicians’ understandings and experience of advance care planning in Norwegian nursing homes: a qualitative study
Authors: Ødbehr Liv , Hov Reidun , Sanaker Harald , Jensen Åsa Serholt , Korup Aina , Sandsdalen Tuva 
Published: June 2024

Abstract
Background
Advance care planning is a way of facilitating conversations with patients about future health care, values, and preferences at end of life. Nursing home physicians have the medical responsibility and the main obligation to facilitate planned meetings with patients. Although there has been a great deal of focus on establishing advance care planning in Norwegian nursing homes, it has yet to be widely implemented. Stated reasons are that the work routines in a nursing home do not include such meetings or that implementation seems complex due to frail patients. The aim of this study is thus to explore how physicians understand and experience advance care planning and follow-up of care plans in Norwegian nursing homes.

Methods
The study has a qualitative research design with a phenomenological-hermeneutic approach based on interviews of twelve nursing home physicians working in community care. Interviews were conducted in February 2023 to May 2023, using a semi-structured interview guide. All interviews were recorded on audio files, transcribed, and analyzed using structural text analysis.

Results
The findings are presented based on the following themes: (1) advance care planning is a dialog and a process, (2) advance care planning implies clarifying mutual expectations, and (3) advance care planning that brings relief and hope to patients is a medical art.

Conclusions
Advance care planning is a complex and dynamic process that implies medical treatment, decisions on treatment level, pain relief, and formulation of care plans where the patient’s self-determination and personal values are respected. It implies an ongoing dialogue between physicians, patients, and their relatives about values such as dignity, self-understanding, social relations, and existential questions at end of life. Advance care planning requires a holistic approach that meets patients’ psychological and existential needs such as comfort, trust, hope, and respect as well as their preferences and concerns.