bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome characteristics of epithelial cells from advanced non‐small cell lung cancer were revealed by single‐cell RNA sequencing
Authors: Qiu Peng , Chen Yutao , Dong Cheng , Xie Juanjuan , Wang Junwu 
Published: September 2023

AbstractBackgroundLung adenocarcinoma (LUAD) is the prevalent malignancy worldwide. The aim is to explore differentially expressed genes (DEGs) associated with immune infiltration and survival time of LUAD patients, and predict transcriptional factors for shedding new light on molecular mechanisms and individual therapy of LUAD.MethodScRNA‐seq data of LUAD patients was downloaded from GSE148071 and analyzed by R packages. The clustering and protein–protein interaction network were constructed for screening DEGs. Gene Set Enrichment Analysis (GSEA) and GO enrichment analysis were performed in epithelial cell subgroups with high differentiation potential. Potential regulatory transcription factors were predicted.ResultsSixteen epithelial cell types were required and top 20 genes were identified on cell subgroup Epi4 with the highest differentiation potential associated with poor prognosis of LUAD in PPI network. GSEA and GO annotation results showed that cell subgroup Epi4 was enriched in the biological processes of cell proliferation and energy metabolism, and positively regulated the function of cell proliferation. TPI1 was significantly highly expressed in LUAD samples (p < .0001). TPI1 demonstrated a negative correlation with the infiltration levels of CD8+ T cells, CD4+ T cells, B cells, and activated mast cells, whilst manifesting a positive correlation with the infiltration levels of resident mast cells, Th2 cells, and MDSC. Epi4 was regulated by transcription factors MXD3 and GATA4.ConclusionOverexpression of TPI1 was identified as a novel biomarker for LUAD, and potential regulatory transcription factors MXD3 and GATA4 regulated the proliferation of LUAD with the poor prognosis, which may serve as potential targets to suppress the proliferation of LUAD.
Glufosinate‐ammonium causes liver injury in zebrafish by blocking the Nrf2 pathway
Authors: Kou Yuhong , Chen Yongping , Feng Tongtong , Chen Luomeng , Wang Hui , Sun Ning , Zhao Shuping , Yang Tianyuan , Jiao Wenjing , Feng Guofeng , Fan Honggang , Zhao Yuan 
Published: September 2023

AbstractGlufosinate‐ammonium (GLA) is a widely used herbicide, but less research has been done on its harmful effects on non‐target organisms, especially aquatic organisms. In this study, 600 adult zebrafish were exposed to different concentration of GLA (0, 1.25, 2.5, 5, 10, and 20 mg/L) for 7 days, and the livers were dissected on the eighth day to examine the changes in liver structure, function, oxidative stress, inflammation, apoptosis, and Nrf2 pathway, and finally to clarify the mechanism of GLA induced liver injury in zebrafish. The levels of alanine aminotransferase, aspartate aminotransferase, reactive oxygen species, malondialdehyde, inflammatory factors (IL‐6 and TNF‐α), and caspase‐3 gradually increased, while the levels of superoxide dismutase, catalase, glutathione, and glutathione peroxidase gradually decreased with the increase of GLA concentration. The Nrf2 pathway was activated at low concentrations (1.25–5 mg/L) and significantly inhibited at high concentrations (10 and 20 mg/L). These results suggested that GLA could cause oxidative stress, inflammation, and apoptosis in zebrafish liver. Therefore, GLA can cause liver injury in zebrafish, and at high concentrations, the inhibition of Nrf2 pathway is one of the important causes of liver injury.
Endometrial polyp in a spayed female dog
Authors: Lai Lik Hang , Jenkins Paul Laurence , Sumner Julia Peta , Marchevsky Andrew Malcolm 
Published: September 2023

AbstractEndometrial polyps are rare benign uterine masses exclusively reported in geriatric, entire, female dogs or spayed female dogs with ovarian remnant syndrome. A 12‐year‐old, female, ovariohysterectomised cocker spaniel was presented for hyporexia, progressive muco‐haemorrhagic vulval discharge, and an ultrasonographically detected caudal abdominal mass. Thoracic and abdominal computed tomography revealed that the mass originated from the uterine stump, with no evidence of metastasis. Surgical excision of the mass was performed, and histopathology of the mass was consistent with an endometrial polyp. The dog was confirmed to be neutered based on the absence of ovarian remnant found on computed tomography and during surgery, and the negative results of both anti‐Mullerian hormone test and human chorionic gonadotropin stimulated progesterone test. The dog fully recovered with complete resolution of clinical signs at 2‐week, 6‐month and 18‐month rechecks. The presenting case highlights the first reported case of an endometrial polyp in a spayed female dog.
NLO QCD predictions for off-shell $$ t\overline{t}W $$ production in association with a light jet at the LHC
Authors: Bi Huan-Yu , Kraus Manfred , Reinartz Minos , Worek Malgorzata 
Published: September 2023

Abstract
In view of the persisting tension between theoretical predictions and the LHC data for the pp → $$ t\overline{t}W $$
t

t
¯

W
± production process, we present the state-of-the-art full off-shell NLO QCD result for pp → $$ t\overline{t}W $$
t

t
¯

W
+j + X. We concentrate on the multi-lepton decay channel at the LHC with $$ \sqrt{s} $$

s

= 13 TeV. In our calculation off-shell top quarks and gauge bosons are described by Breit-Wigner propagators, furthermore, double-, single- as well as non-resonant top-quark contributions along with all interference effects are consistently incorporated at the matrix element level. We present results for both integrated and differential fiducial cross sections for various renormalisation and factorisation scale settings and different PDF sets. With a fairly inclusive choice of cuts and regardless of the scale and PDF choice, non-flat differential $$ \mathcal{K} $$
K
-factors are obtained for many observables that we have examined. Since from an experimental point of view, both processes pp → $$ t\overline{t}W $$
t

t
¯

W
±j + X and pp → $$ t\overline{t}W $$
t

t
¯

W
± + X consist of similar final states we investigate the effect of additional jet activity on the integrated and differential fiducial cross sections. For this purpose, the normalised differential distributions for pp → e+νeμ−$$ \overline{\nu} $$

ν
¯

μτ+ντ$$ b\overline{b} $$
b

b
¯

j + X and pp → e+νeμ−$$ \overline{\nu} $$

ν
¯

μτ+ντ$$ b\overline{b} $$
b

b
¯

+ X are compared. The theoretical results for the latter process are also recalculated.
Investigation of the scale dependence in the MSR and $$ \overline{\textrm{MS}} $$ top quark mass schemes for the $$ \textrm{t}\overline{\textrm{t}} $$ invariant mass differential cross section using LHC data
Authors: Mäkelä Toni , Hoang André H. , Lipka Katerina , Moch Sven-Olaf 
Published: September 2023

Abstract
The computation of the single-differential top quark-antiquark pair ($$ \textrm{t}\overline{\textrm{t}} $$
t

t
¯

) production cross section at NLO in the fixed-order expansion is examined consistently using the MSR and $$ \overline{\textrm{MS}} $$

MS
¯

short-distance top quark mass schemes. A thorough investigation of the dependence of different regions of the $$ \textrm{t}\overline{\textrm{t}} $$
t

t
¯

invariant mass spectrum on the renormalization scales R and μm of the MSR mass $$ {m}_{\textrm{t}}^{\textrm{MSR}} $$

m
t
MSR

(R) and $$ \overline{\textrm{MS}} $$

MS
¯

mass $$ \overline{m} $$

m
¯

t(μm), respectively, is carried out. We demonstrate that a scale choice of R ~ 80 GeV is important for the stability of the cross-section predictions for the low $$ \textrm{t}\overline{\textrm{t}} $$
t

t
¯

invariant mass range, which is important for a reliable extraction of the top quark mass. Furthermore, a choice of semi-dynamical renormalization and factorization scales is preferred. These findings are expected to remain valid once non-relativistic quasi-bound state effects are included in the low invariant mass region.
Wheat (Triticum aestivum) chromosome 6D harbours the broad spectrum common bunt resistance gene Bt11
Authors: Lunzer Magdalena , Buerstmayr Maria , Grausgruber Heinrich , Müllner Almuth Elise , Fallbacher Iris , Buerstmayr Hermann 
Published: September 2023

Abstract
Key message
A major QTL on chromosome 6DL corresponding to bunt resistance gene Bt11 was identified in four mapping populations generated through crosses with Bt11-carriers PI 166910 and M822123.

Abstract
Common bunt in wheat has witnessed a renaissance with the rise of organic agriculture that began in the 1980s. The abandonment of systemic fungicides in organic farming, together with a lack of resistant cultivars, has led to wide-spread problems due to common bunt infections. Knowledge about genetic sources for resistance is still scarce and only few of the known bunt resistance factors are currently used in breeding. We therefore aimed to map the resistance factor harboured by the Turkish landrace PI 166910, which is the resistance donor for the Bt11 bunt differential line. Four mapping populations (MPs) with 96–132 recombinant inbred lines (RILs) were phenotyped for common bunt resistance over 2, 3 or 4 years with one or two local bunt populations and genotyped with the 25K SNP array. A major bunt resistance locus on the distal end of chromosome 6D designated QBt.ifa-6DL was identified in all MPs and experiments. Additional QTL contributing to resistance were detected on chromosomes 4B, 1A, 1B, 2A and 7B. QBt.ifa-6DL mapped to a region overlapping with the Bt9-locus identified in previous studies, but results indicate that QBt.ifa-6DL is different from Bt9 and convincing evidence from haplotype comparisons suggests that it represents the Bt11 resistance allele. Markers for the distal region of chromosome 6D between 492.6 and 495.2 Mbp can be used to select for QBt.ifa-6DL. This resistance factor confers high and stable resistance against common bunt and should be integrated into organic and low-input wheat breeding programs.
Thiopental and decompressive craniectomy as last-tier ICP-treatments in aneurysmal subarachnoid hemorrhage: is functional recovery within reach?
Authors: Björk Sofie , Hånell Anders , Ronne-Engström Elisabeth , Stenwall Anton , Velle Fartein , Lewén Anders , Enblad Per , Svedung Wettervik Teodor 
Published: September 2023

AbstractThe study aimed to investigate the indication and functional outcome after barbiturates and decompressive craniectomy (DC) as last-tier treatments for elevated intracranial pressure (ICP) in aneurysmal subarachnoid hemorrhage (aSAH). This observational study included 891 aSAH patients treated at a single center between 2008 and 2018. Data on demography, admission status, radiology, ICP, clinical course, and outcome 1-year post-ictus were collected. Patients treated with thiopental (barbiturate) and DC were the main target group.Thirty-nine patients (4%) were treated with thiopental alone and 52 (6%) with DC. These patients were younger and had a worse neurological status than those who did not require these treatments. Before thiopental, the median midline shift was 0 mm, whereas basal cisterns were compressed/obliterated in 66%. The median percentage of monitoring time with ICP > 20 mmHg immediately before treatment was 38%, which did not improve after 6 h of infusion. Before DC, the median midline shift was 10 mm, and the median percentage of monitoring time with ICP > 20 mmHg before DC was 56%, which both significantly improved postoperatively. At follow-up, 52% of the patients not given thiopental or operated with DC reached favorable outcome, whereas this occurred in 10% of the thiopental and DC patients.In summary, 10% of the aSAH cohort required thiopental, DC, or both. Thiopental and DC are important integrated last-tier treatment options, but careful patient selection is needed due to the risk of saving many patients into a state of suffering.
Best practices for sign language technology research
Authors: Fox Neil , Woll Bencie , Cormier Kearsy 
Published: September 2023

AbstractResearch on sign language technology (SLT) has steadily increased in recent decades, and yet, common mistakes and pitfalls have significantly hindered progress in the field. The purpose of this paper is to examine some of the most prominent issues and suggest practical steps to overcome them, outlining the best practices to consider when conducting SLT research. These practices cluster around the five following issues: (1) knowledge of the specific sign language at the centre of the research and of sign languages more generally; (2) involving deaf people at the centre of research, including researchers who are themselves deaf; (3) motivations of the researcher and the relationship to the views of the sign language community; (4) what sign language data needs to be considered; (5) full recognition of the challenges posed by such research.
Different patterns of failure in two treatment regimens for primary central nervous system lymphoma, a retrospective analysis of 124 cases in Taiwan
Authors: Chuang Chin-Hsuan , Kuo Ming-Chung , Chang Hung , Wu Jin-Hou , Hung Yu-Shin , Ou Che-Wei , Lin Tung-Liang , Su Yi-Jiun , Ong Yuen-Chin , Shih Lee-Yung , Kao Hsiao-Wen 
Published: September 2023

AbstractTo explore prognostic factors and outcomes of primary central nervous system lymphoma (PCNSL) of diffuse large B-cell lymphoma (DLBCL) in Taiwan, 124 PCNSL-DLBCL patients (from 1995 to 2021) were retrospectively analyzed. Mainly, two treatment modalities including sandwich chemoradiotherapy and modified MATRix regimen were employed in these patients. Overall survival (OS) was determined by log-rank test and time-dependent Cox analysis. Median OS of all patients was 27.1 months. 47 (37.9%) patients who underwent sandwich chemoradiotherapy had a complete remission (CR) rate of 87.2%, median OS of 53.9 months, and progression free survival (PFS) of 42.9 months. 11 (8.9%) patients who underwent modified MATRix regimen had CR rate of 72.7%, median OS of 18.9, and PFS of 11.2 months. There are no significant OS differences between treatment groups or addition of Rituximab. Patients treated with the modified MATRix regimen experienced a higher early mortality rate followed by a survival plateau. IELSG low-risk group had significantly improved OS and PFS than IELSG intermediate- or high-risk group. In multivariant analysis, age > 60 years old and bilateral cerebral lesions are associated with significantly inferior OS. Sandwich chemoradiotherapy demonstrated better early survival and reduced treatment-related toxicity for PCNSL patients compared to the modified MATRix regimen. However, the long-term follow-up revealed a higher rate of treatment failure events in the sandwich chemoradiotherapy group. IELSG and MSKCC scores served as reliable risk assessment models. Incorporating bilateral cerebral lesions as a risk factor further improved risk evaluation.
Hybrides Leiten im Psychodrama
Authors: Gastauer Dirk , Hunger Mathias 
Published: September 2023

ZusammenfassungIm Rahmen ihrer Ausbildung in der Psychodrama-Oberstufe haben die Autoren in der Zeit der Corona-Pandemie einige Erfahrungen sowohl im digitalen als auch hybriden Leiten gesammelt. Hierzu gehört, dass während eines Seminars in Präsenz auch digital zugeschaltete Teilnehmende eingebunden werden. In diesem Beitrag der Zeitschrift für Psychodrama und Soziometrie stellen sie diese Erfahrungen dar, gehen auf Probleme und Lösungsansätze ein und weisen auf offene Fragen hin.
Green synthesis and characterization of aluminum oxide nanoparticles using Phoenix dactylifera seed extract along with antimicrobial activity, phytotoxicity, and cytological effects on Vicia faba seeds
Authors: Saleh Ahmed K. , Shaban Abdelghany S. , Diab Mohamed A. , Debarnot Dominique , Elzaref Ahmed S. 
Published: September 2023

AbstractThe present study assessed the green synthesis of aluminum oxide nanoparticles (Al2O3-NPs) by using aluminum (Al) foil waste as an Al source and date palm seed extract as a reducing and stabilizing agent. Several methodologies were employed to investigate Al2O3-NPs, encompassing X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and energy-dispersive X-ray (EDX) analysis. The UV–visible spectroscopy analysis revealed the presence of an absorption peak at a wavelength of 264 nm, providing evidence for the successful green synthesis of the Al2O3-NPs. The XRD analysis revealed that the average size of the Al2O3-NPs was 32 ± 2.57 nm and had a rhombohedral structure. The EDX facilitated the identification of the elemental composition of the sample, which was found to consist of 40.37% Al and 31.56% O, confirming the high purity of the Al2O3-NPs powder. Furthermore, it was noted that the Al2O3-NPs exhibited the greatest antibacterial efficacy against Candida albicans (21 ± 1.85 mm), but no discernible antimicrobial effect was recorded against Klebsiella pneumoniae at higher concentrations of Al2O3-NPs. No significant variation in the germination of faba bean seeds was observed upon treatment with Al2O3-NPs. The observed mitotic index in the treatment group was determined to be significantly lower compared to the control cells, based on the duration and dosage of Al2O3-NP exposure. In contrast, for micronuclei (MN) and the prevalence of chromosomal abnormalities, there is a noticeable upward trajectory in this phenomenon. Finally, Al2O3-NPs are employed in a variety of applications, such as biomedical and agriculture.
Host-derived growth factors drive ERK phosphorylation and MCL1 expression to promote osteosarcoma cell survival during metastatic lung colonization
Authors: McAloney Camille A. , Makkawi Rawan , Budhathoki Yogesh , Cannon Matthew V. , Franz Emily M. , Gross Amy C. , Cam Maren , Vetter Tatyana A. , Duhen Rebekka , Davies Alexander E. , Roberts Ryan D. 
Published: September 2023

Abstract
Purpose
For patients with osteosarcoma, disease-related mortality most often results from lung metastasis—a phenomenon shared with many solid tumors. While established metastatic lesions behave aggressively, very few of the tumor cells that reach the lung will survive. By identifying mechanisms that facilitate survival of disseminated tumor cells, we can develop therapeutic strategies that prevent and treat metastasis.

Methods
We analyzed single cell RNA-sequencing (scRNAseq) data from murine metastasis-bearing lungs to interrogate changes in both host and tumor cells during colonization. We used these data to elucidate pathways that become activated in cells that survive dissemination and identify candidate host-derived signals that drive activation. We validated these findings through live cell reporter systems, immunocytochemistry, and fluorescent immunohistochemistry. We then validated the functional relevance of key candidates using pharmacologic inhibition in models of metastatic osteosarcoma.

Results
Expression patterns suggest that the MAPK pathway is significantly elevated in early and established metastases. MAPK activity correlates with expression of anti-apoptotic genes, especially MCL1. Niche cells produce growth factors that increase ERK phosphorylation and MCL1 expression in tumor cells. Both early and established metastases are vulnerable to MCL1 inhibition, but not MEK inhibition in vivo. Combining MCL1 inhibition with chemotherapy both prevented colonization and eliminated established metastases in murine models of osteosarcoma.

Conclusion
Niche-derived growth factors drive MAPK activity and MCL1 expression in osteosarcoma, promoting metastatic colonization. Although later metastases produce less MCL1, they remain dependent on it. MCL1 is a promising target for clinical trials in both human and canine patients.
Information flow-based fuzzy cognitive maps with enhanced interpretability
Authors: Tyrovolas Marios , Liang X. San , Stylios Chrysostomos 
Published: September 2023

AbstractFuzzy Cognitive Maps (FCMs) are a graph-based methodology successfully applied for knowledge representation of complex systems modelled through an interactive structure of nodes connected with causal relationships. Due to their flexibility and inherent interpretability, FCMs have been used in various modelling and prediction tasks to support human decisions. However, a notable limitation of FCMs is their susceptibility to inadvertently capturing spurious correlations from data, undermining their prediction accuracy and interpretability. In addressing this challenge, our primary contribution is the introduction of a novel framework for constructing FCMs using the Liang-Kleeman Information Flow (L-K IF) analysis, a quantitative causality analysis rigorously derived from first principles. The novelty of the proposed approach lies in the identification of actual causal relationships from the data using an automatic causal search algorithm. These relationships are subsequently imposed as constraints in the FCM learning procedure to rule out spurious correlations and improve the aggregate predictive and explanatory power of the model. Numerical simulations validate the superiority of our method against state-of-the-art FCM-based models, thereby bolstering the reliability, accuracy, and interpretability of FCMs.
Closed-Form Wave Dispersion Relationships for Ordinary State-Based Peridynamics
Authors: Wang Bingquan , Oterkus Selda , Oterkus Erkan 
Published: September 2023

AbstractPeridynamics (PD) is a new continuum mechanics formulation introduced to overcome limitations of classical continuum mechanics (CCM). This is mainly achieved by using integro-differential equations rather than partial differential equations. Another important difference of PD is its nonlocal nature with respect to local characteristic of CCM. Moreover, it has a length scale parameter, horizon, defining the range of nonlocal interactions between material points. This nonclassical behaviour also shows itself for dispersion relationships. As opposed to linear dispersion relationships for CCM, PD dispersion relationships are non-linear similar to the observed in experiments. In this study, closed-form dispersion relationships are provided for ordinary state-based peridynamics which is one of the most common PD formulations. Finally, derived closed-form solutions are used to demonstrate the dispersion relationships for various material systems including copper, gold, silver and platinum.
Social Norms Predict Bullying: Evidence from an Anti-Bullying Intervention Trial in Indonesia
Authors: Zaneva Mirela , Minnick Emilie , Nahar  , Ginting Valentina , Aryani Farida , Ohan Faridah , Haryanti Rina Herlina , Winarna Sri , Arsianto Yuli , Budiyawati Hening , Widowati Evi , Saraswati Rika , Kristianto Yuliana , Suryani Yulinda Erma , Ulum Derry Fahrizal , Bowes Lucy 
Published: September 2023

AbstractSocial norms pertaining to negative or violent interpersonal behaviours constitute a promising target for programs designed to reduce bullying. Yet, there is a lack of evidence on anti-bullying programs targeting social norms in non-Western, low- and middle-income countries. Here, we report findings on the relationship between social norms and bullying from one such large-scale program, the feasibility trial of the ROOTS-Indonesia intervention. This intervention was delivered across 12 secondary schools in two different regions in Indonesia. We report findings based on a total of 7,203 students at baseline (in South Sulawesi, n = 1901, mean age = 13 years, 53% female; and in Central Java, n = 5302, mean age = 13.3 years, 48% female). Via a multilevel analytic approach, we found consistent evidence that the extent to which negative behaviours were considered normative by students was associated with how much they would engage in bullying, both as perpetrators and as victims. Our data reveal some encouraging trends suggesting the ROOTS-Indonesia intervention reduced negative social norms. We note a trend such that where social norms decreased the most at follow-up, the rates of bullying similarly decreased the most. Overall, we provide further evidence that social norms are a promising avenue for the reduction of negative interpersonal behaviours.