bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptome analysis of two Daphnia galeata genotypes displaying contrasting phenotypic variation induced by fish kairomones in the same environment of the Han River, Korea
Authors: Choi Tae-June , Han Seung-Min , Malik Adeel , Kim Chang-Bae 
Published: October 2023

AbstractBackgroundPhenotypic plasticity is a crucial adaptive mechanism that enables organisms to modify their traits in response to changes in their environment. Predator-induced defenses are an example of phenotypic plasticity observed across a wide range of organisms, from single-celled organisms to vertebrates. In addition to morphology and behavior, these responses also affect life-history traits. The crustaceanDaphnia galeatais a suitable model organism for studying predator-induced defenses, as it exhibits life-history traits changes under predation risk. To get a better overview of their phenotypic plasticity under predation stress, we conducted RNA sequencing on the transcriptomes of two KoreanDaphnia galeatagenotypes, KE1, and KB11, collected in the same environment.ResultsWhen exposed to fish kairomones, the two genotypes exhibited phenotypic variations related to reproduction and growth, with opposite patterns in growth-related phenotypic variation. From both genotypes, a total of 135,611 unigenes were analyzed, of which 194 differentially expressed transcripts (DETs) were shared among the two genotypes under predation stress, which showed consistent, or inconsistent expression patterns in both genotypes. Prominent DETs were related to digestion and reproduction and consistently up-regulated in both genotypes, thus associated with changes in life-history traits. Among the inconsistent DETs, transcripts encode vinculin (VINC) and protein obstructor-E (OBST-E), which are associated with growth; these may explain the differences in life-history traits between the two genotypes. In addition, genotype-specific DETs could explain the variation in growth-related life-history traits between genotypes, and could be associated with the increased body length of genotype KE1.ConclusionsThe current study allows for a better understanding of the adaptation mechanisms related to reproduction and growth of two KoreanD. galeatagenotypes induced by predation stress. However, further research is necessary to better understand the specific mechanisms by which the uncovered DETs are related with the observed phenotypic variation in each genotype. In the future, we aim to unravel the precise adaptive mechanisms underlying predator-induced responses.
Epidemiology and clinical characteristics of patients with carbapenem-resistant enterobacterales infections: experience from a large tertiary care center in a developing country
Authors: Aiesh Banan M. , Maali Yazan , Qandeel Farah , Omarya Siwar , Taha Shatha Abu , Sholi Suha , Sabateen Ali , Taha Adham Abu , Zyoud Sa’ed H. 
Published: October 2023

Abstract
Background
Carbapenem-resistant Enterobacterales (CREs) are a significant source of healthcare-associated infections. These bacteria are difficult to treat and have a high mortality rate due to high rates of antibiotic resistance. These pathogens are also linked to major outbreaks in healthcare institutions especially those with limited resources in infection prevention and control (IPC). Therefore, our study aimed to describe the epidemiology and clinical characteristics of patients with carbapenem-resistant Enterobacteriaceae in a referral hospital in a developing country.

Methods
This was a retrospective cross-sectional study that included 218 patients admitted to An-Najah National University Hospital between January 1, 2021, and May 31, 2022. The target population was all patients with CRE infection or colonization in the hospital setting.

Results
Of the 218 patients, 135 had CR-Klebsiella pneumoniae (61.9%), and 83 had CR-Escherichia coli (38.1%). Of these, 135 were male (61.9%) and 83 were female (38.1%), with a median age of 51 years (interquartile range 24–64). Malignancy was a common comorbidity in 36.7% of the patients. Approximately 18.3% of CRE patients were obtained from patients upon admission to the emergency department, the largest percentage among departments. Most CRE pathogens were isolated from rectal swabs, accounting for 61.3%. Among the 218 patients, colistin was the most widely used antimicrobial agent (13.3%). CR- E. coli showed resistance to amikacin in 23.8% of the pathogens tested and 85.7% for trimethoprim/sulfamethoxazole compared to CR- K. pneumonia, for which the resistance to trimethoprim/sulfamethoxazole was 74.1%, while for amikacin it was 64.2%. Regarding meropenem minimum inhibitory concentration, 85.7% of CR- E. coli were greater than 16 µg/mL compared to 84% of CR- K. pneumonia isolates.

Conclusion
This study found that CRE is frequently reported in this tertiary care setting, implying the presence of selective pressure and transmission associated with healthcare setting. The antibiotics tested showed a variety of resistance rates, with CR-K. pneumoniae being more prevalent than CR-E. coli, and exhibiting an extremely high resistance pattern to the available therapeutic options.
Comparison of bacterial culture with BioFire® FilmArray® multiplex PCR screening of archived cerebrospinal fluid specimens from children with suspected bacterial meningitis in Nigeria
Authors: Obaro S. , Hassan-Hanga F. , Medugu N. , Olaosebikan R. , Olanipekun G. , Jibir B. , Gambo S. , Ajose Theresa , Duru Carissa , Ebruke B. , Davies H. D. 
Published: October 2023

Abstract
Background
Diagnosis of bacterial meningitis remains a challenge in most developing countries due to low yield from bacterial culture, widespread use of non-prescription antibiotics, and weak microbiology laboratories. The objective of this study was to compare the yield from standard bacterial culture with the multiplex nested PCR platform, the BioFire® FilmArray® Meningitis/Encephalitis Panel (BioFire ME Panel), for cases with suspected acute bacterial meningitis.

Methods
Following Gram stain and bacterial culture on cerebrospinal fluid (CSF) collected from children aged less than 5 years with a clinical suspicion of acute bacterial meningitis (ABM) as defined by the WHO guidelines, residual CSF specimens were frozen and later tested by BioFire ME Panel.

Results
A total of 400 samples were analyzed. Thirty-two [32/400 (8%)] of the specimens were culture positive, consisting of; three Salmonella spp. (2 Typhi and 1 non-typhi), three alpha hemolytic Streptococcus, one Staphylococcus aureus, six Neisseria meningitidis, seven Hemophilus influenzae, 11 Streptococcus pneumoniae and 368 were culture negative. Of the 368 culture-negative specimens, the BioFire ME Panel detected at least one bacterial pathogen in 90 (24.5%) samples, consisting of S. pneumoniae, N. meningitidis and H. influenzae, predominantly. All culture positive specimens for H. influenzae, N. meningitidis and S. pneumoniae also tested positive with the BioFire ME Panel. In addition, 12 specimens had mixed bacterial pathogens identified. For the first time in this setting, we have data on the viral agents associated with meningitis. Single viral agents were detected in 11 (2.8%) samples while co-detections with bacterial agents or other viruses occurred in 23 (5.8%) of the samples.

Conclusions
The BioFire® ME Panel was more sensitive and rapid than culture for detecting bacterial pathogens in CSF. The BioFire® ME Panel also provided for the first time, the diagnosis of viral etiologic agents that are associated with meningoencephalitis in this setting. Institution of PCR diagnostics is recommended as a routine test for suspected cases of ABM to enhance early diagnosis and optimal treatment.
Predicting response to CCRT for esophageal squamous carcinoma by a radiomics-clinical SHAP model
Authors: Cheng Xu , Zhang Yuxin , Zhu Min , Sun Ruixia , Liu Lingling , Li Xueling 
Published: October 2023

Abstract
Background
Radical concurrent chemoradiotherapy (CCRT) is frequently used as the first-line treatment for patients with locally advanced esophageal cancer. Unfortunately, some patients respond poorly. To predict response to radical concurrent chemoradiotherapy in pre-treatment patients with esophageal squamous carcinoma (ESCC), and compare the predicting efficacies of radiomics features of primary tumor with or without regional lymph nodes, we developed a radiomics-clinical model based on the positioning CT images. Finally, SHapley Additive exPlanation (SHAP) was used to explain the models.

Methods
This retrospective study enrolled 105 patients with medically inoperable and/or unresectable ESCC who underwent radical concurrent chemoradiotherapy (CCRT) between October 2018 and May 2023. Patients were classified into responder and non-responder groups with RECIST standards. The 11 recently admitted patients were chosen as the validation set, previously admitted patients were randomly split into the training set (n = 70) and the testing set (n = 24). Primary tumor site (GTV), the primary tumor and the uninvolved lymph nodes at risk of microscopic disease (CTV) were identified as Regions of Interests (ROIs). 1762 radiomics features from GTV and CTV were respectively extracted and then filtered by statistical differential analysis and Least Absolute Shrinkage and Selection Operator (LASSO). The filtered radiomics features combined with 13 clinical features were further filtered with Mutual Information (MI) algorithm. Based on the filtered features, we developed five models (Clinical Model, GTV Model, GTV-Clinical Model, CTV Model, and CTV-Clinical Model) using the random forest algorithm and evaluated for their accuracy, precision, recall, F1-Score and AUC. Finally, SHAP algorithm was adopted for model interpretation to achieve transparency and utilizability.

Results
The GTV-Clinical model achieves an AUC of 0.82 with a 95% confidence interval (CI) of 0.76–0.99 on testing set and an AUC of 0.97 with a 95% confidence interval (CI) of 0.84–1.0 on validation set, which are significantly higher than those of other models in predicting ESCC response to CCRT. The SHAP force map provides an integrated view of the impact of each feature on individual patients, while the SHAP summary plots indicate that radiomics features have a greater influence on model prediction than clinical factors in our model.

Conclusion
GTV-Clinical model based on texture features and the maximum diameter of lesion (MDL) may assist clinicians in pre-treatment predicting ESCC response to CCRT.
Dissection of paracrine/autocrine interplay in lung tumor microenvironment mimicking cancer cell-monocyte co-culture models reveals proteins that promote inflammation and metastasis
Authors: Amin Asif , Koul Aabid Mustafa , Wani Umer Majeed , Farooq Faizah , Amin Basit , Wani Zubair , Lone Asif , Qadri Ayub , Qadri Raies A. 
Published: October 2023

Abstract
Background
Tumor cell-monocyte interactions play crucial roles in shaping up the pro-tumorigenic phenotype and functional output of tumor-associated macrophages. Within the tumor microenvironment, such heterotypic cell–cell interactions are known to occur via secretory proteins. Secretory proteins establish a diabolic liaison between tumor cells and monocytes, leading to their recruitment, subsequent polarization and consequent tumor progression.

Methods
We co-cultured model lung adenocarcinoma cell line A549 with model monocytes, THP-1 to delineate the interactions between them. The levels of prototypical pro-inflammatory cytokines like TNF-𝛼, IL-6 and anti-inflammatory cytokines like IL-10 were measured by ELISA. Migration, invasion and attachment independence of lung cancer cells was assessed by wound healing, transwell invasion and colony formation assays respectively. The status of EMT was evaluated by immunofluorescence. Identification of secretory proteins differentially expressed in monocultures and co-culture was carried out using SILAC LC–MS/MS. Various insilico tools like Cytoscape, Reacfoam, CHAT and Kaplan–Meier plotter were utilized for association studies, pathway analysis, functional classification, cancer hallmark relevance and predicting the prognostic potential of the candidate secretory proteins respectively.

Results
Co-culture of A549 and THP-1 cells in 1:10 ratio showed early release of prototypical pro-inflammatory cytokines TNF-𝛼 and IL-6, however anti-inflammatory cytokine, IL-10 was observed to be released at the highest time point. The conditioned medium obtained from this co-culture ratio promoted the migration, invasion and colony formation as well as the EMT of A549 cells. Co-culturing of A549 with THP-1 cells modulated the secretion of proteins involved in cell proliferation, migration, invasion, EMT, inflammation, angiogenesis and inhibition of apoptosis. Among these proteins Versican, Tetranectin, IGFBP2, TUBB4B, C2 and IFI30 were found to correlate with the inflammatory and pro-metastatic milieu observed in our experimental setup. Furthermore, dysregulated expression of these proteins was found to be associated with poor prognosis and negative disease outcomes in lung adenocarcinoma compared to other cancer types. Pharmacological interventions targeting these proteins may serve as useful therapeutic approaches in lung adenocarcinoma.

Conclusion
In this study, we have demonstrated that the lung cancer cell-monocyte cross-talk modulates the secretion of IFI30, RNH1, CLEC3B, VCAN, IGFBP2, C2 and TUBB4B favoring tumor growth and metastasis.
Health-related quality of life of metastatic prostate cancer patients treated with prostate Radiotherapy
Authors: Ayoub Heba Maged , Zamzam Maha Lotfy , Elsemary Eman Essam , Hassanin Ihab Mohamed , Elsayed Fifi Mostafa 
Published: October 2023

Abstract
Background
The impact of prostate radiotherapy on patient-reported health-related quality of life (HRQoL) significantly influences the outcomes of metastatic prostate cancer. We measured and compared HRQoL of metastatic prostate cancer patients who received cytoreductive prostate radiotherapy.

Methods
Between November 23, 2020, and November 21, 2022, we recruited 70 metastatic prostate cancer patients at the Department of Clinical Oncology at Suez Canal University Hospital. Patients were eligible if they had synchronous and metachronous histopathological confirmed metastatic adenocarcinoma and an Eastern Cooperative Oncology Group performance status ≤ 2. Random allocation was performed for either definitive local radiotherapy concurrent with the standard androgen deprivation therapy (ADT) or to the standard ADT alone. Definitive radiotherapy was delivered conventionally (70 Gy/35 fractions) or through the hypofractionated regimen (55 Gy/20 fractions). Patients completed the comprehensive European Organization for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ-PR25) at baseline, then at three-month intervals for one year. The primary endpoint was patient-reported HRQoL, with secondary endpoints including toxicity and radiographic progression-free survival (rPFS). Mean HRQoL scores between groups were compared using the independent samples t-test.

Results
We observed clinically significant improvements in urinary and bowel functions between baseline, 3-month, 6-month, and 12-month intervals after receiving definitive prostate radiotherapy. Patients in the radiotherapy group had significantly lower urinary symptoms scores than the control group. However, sexual activity and functioning showed significant deterioration.

Conclusion
Cytoreductive prostate radiotherapy in metastatic prostate cancer patients significantly improved urinary functioning, preserved bowel functioning but was associated with worsening of sexual functioning.

Trial Registration
This trial was registered on (27/04/2023) with pactr.samrc.ac.za, PACTR202305854600529, URL: https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=25510.
A novel CACNA1S gene variant in a child with hypokalemic periodic paralysis: a case report and literature review
Authors: Zhou Wen , Zhao Peilin , Gao Jian , Zhang Yunjian 
Published: October 2023

Abstract
Background
The CACNA1S gene encodes the alpha 1 S-subunit of the voltage-gated calcium channel, which is primarily expressed in the skeletal muscle cells. Pathogenic variants of CACNA1S can cause hypokalemic periodic paralysis (HypoPP), malignant hyperthermia susceptibility, and congenital myopathy. We aimed to study the clinical and molecular features of a male child with a CACNA1S variant and depict the molecular sub-regional characteristics of different phenotypes associated with CACNA1S variants.

Case presentation
We presented a case of HypoPP with recurrent muscle weakness and hypokalemia. Genetic analyses of the family members revealed that the proband had a novel c.497 C > A (p.Ala166Asp) variant of CACNA1S, which was inherited from his father. The diagnosis of HypoPP was established in the proband as he met the consensus diagnostic criteria. The patient and his parents were informed to avoid the classical triggers of HypoPP. The attacks of the patient are prevented by lifestyle changes and nutritional counseling. We also showed the molecular sub-regional location of the variants of CACNA1S which was associated with different phenotypes.

Conclusions
Our results identified a new variant of CACNA1S and expanded the spectrum of variants associated with HypoPP. Early genetic diagnosis can help avoid diagnostic delays, perform genetic counseling, provide proper treatment, and reduce morbidity and mortality.
Measuring the neglected anxiety disorder: validation of the social anxiety spectrum-short version (SHY-SV) questionnaire
Authors: Dell’Osso Liliana , Cremone Ivan Mirko , Nardi Benedetta , Amatori Giulia , Bonelli Chiara , Gravina Davide , Benedetti Francesca , Del Prete Luca , Massimetti Gabriele , Carpita Barbara 
Published: October 2023

Abstract
Background
In the recent years, a growing body of literature stressed the importance of a dimensional perspective on mental disorders. In particular, since its conceptualization, one of the main concerns in the field of Social Anxiety Disorder (SAD) has been the definition of a diagnostic threshold, leading to the suggestion that SAD may be more properly classified as a spectrum of severity rather than a discrete disorder based on subjectively determined threshold. The purpose of the current research is to evaluate the psychometric qualities of the Social Anxiety Spectrum - Short Version (SHY-SV), a novel questionnaire designed to measure the complete range of social anxiety symptoms, from overt manifestations to subthreshold ones.

Methods
42 subjects with a clinical diagnosis of social anxiety disorder (SAD) according to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5), 43 subjects with a clinical diagnosis of Obsessive-Compulsive Disorder (OCD) and 60 individuals without current or lifetime mental disorders (HC) were recruited from the Psychiatric Clinic of the University of Pisa. Subjects were assessed with the SCID-5, Liebowitz Social Anxiety Scale (LSAS) and the SHY-SV.

Results
SHY-SV showed strong internal consistency, and both the total and domain scores had great test-retest reliability. The Pearson’s coefficients for the SHY-SV domain scores ranged from 0.391 to 0.933, and they were positively and significantly correlated with one another (p 0.001). All the SHY-SV domain scores were highly correlated with the SHY-SV total score. Results from of the correlation coefficients between SHY-SV and alternative measures of SAD were all significant and positive. Significant differences among diagnostic groups on both SAD-SV domains and total scores were found. SAD-SV total score increased significantly and progressively from HCs, to the OCD up to the SAD group which showed the highest values.

Conclusion
The SHY-SV demonstrated significant convergent validity with other dimensional SAD measures, great internal consistency, and test-retest reliability. With an increasing score gradient from healthy controls to patients with OCD to those with SAD, the questionnaire performed differently in each of the three diagnostic categories.
Relationship between perceived coercion and perceived justification of coercive measures – secondary analysis of a randomized-controlled trial
Authors: Wullschleger Alexandre , Vandamme Angelika , Mielau Juliane , Heinz Andreas , Bermpohl Felix , Mahler Lieselotte , Montag Christiane 
Published: October 2023

Abstract
Background
Subjective perception of coercion has gained attention as an important outcome. However, little is known about its relation to patients’ appraisal of the justification of coercive measures. The present study aims to analyze the relationship between patients’ appraisal of the justification of coercive measures and their level of perceived coercion.

Methods
This study presents a secondary analysis of the results of a multi-center RCT conducted to evaluate the effects of post-coercion review. Patients who experienced at least one coercive measure during their hospital stay were included in the trial. Participants’ appraisal of the justification of coercive measures was categorized into patient-related and staff-related justifications. Subjective coercion was assessed using the Coercion Experience Scale (CES) and used as dependent variable in a multivariate regression model.

Results
97 participants who completed the CES were included in the analysis. CES scores were significantly associated with the perception of the coercive measure as justified by staff-related factors (B = 0,540, p < 0,001), as well as with higher level of negative symptoms (B = 0,265, p = 0,011), and with mechanical restraint compared to seclusion (B=-0,343, p = 0,017).

Conclusions
Patients’ perceptions of coercive measures as justified by staff-related factors such as arbitrariness or incompetence of staff are related to higher levels of perceived coercion. Multiprofessional efforts must be made to restrict the use of coercive measures and to ensure a transparent and sustainable decision-making process, particularly with patients showing high levels of negative symptoms. Such key elements should be part of all coercion reduction programs.