bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scoring scheme for Comparative Ranking of impact potential of chemical Alternatives (SCoRA)
Authors: Nendza Monika , Hahn Stefan , Klein Michael , Klaschka Ursula , Gabbert Silke 
Published: February 2023

Abstract

Background
Replacing hazardous chemicals with safer alternatives is essential for a toxic-free environment. To avoid regrettable substitution, a comparison of the entire spectrum of potential impacts of the candidate for substitution with those of the available alternatives is required. A particular challenge is to also capture yet unknown long-term impacts of (very) persistent chemicals, including but not limited to PBT and CMR properties.

Results
For a flexible and transparent comparative ranking of the impact potential of chemical alternatives, we propose a concern-based scoring scheme (Scoring scheme for Comparative Ranking of chemical Alternatives, SCoRA). The approach accounts for hazards due to ecotoxicity in water/sediment and soil, and effects on human health such as CMR properties and endocrine disruption. This is combined with exposure-related information in terms of expected environmental pollution stock levels. The SCoRA approach is illustrated with case study chemicals of very high concern (15 SVHC, mostly PBT, representing different chemical classes with different modes of bioaccumulation and toxicity). A comparison of PBT substances reveals that SCoRA goes well beyond binary screening criteria (PBT: yes/no), showing that PBT substances are all of very high concern, although their impact profiles can be substantially different. Ordinal scores support a detailed characterisation of their potential for long-term impacts. Furthermore, SCoRA enables a coherent comparative assessment of substances with different primary concerns, for example PBTness and endocrine disruption.

Conclusions
SCoRA complements existing and established tools such as comparative risk assessment. It is particularly useful, when, for example, only limited data are available or when risk assessment is not feasible, as in the case of persistent chemicals. A strength of SCoRA is that the relative contributions of the impact components determining the concern can be visualised with a heatmap and fingerprints. This facilitates communication among scientists, regulators, risk managers, stakeholders and the public.
ConanVarvar: a versatile tool for the detection of large syndromic copy number variation from whole-genome sequencing data
Authors: Gudkov Mikhail , Thibaut Loïc , Khushi Matloob , Blue Gillian M. , Winlaw David S. , Dunwoodie Sally L. , Giannoulatou Eleni 
Published: February 2023

Abstract
Background
A wide range of tools are available for the detection of copy number variants (CNVs) from whole-genome sequencing (WGS) data. However, none of them focus on clinically-relevant CNVs, such as those that are associated with known genetic syndromes. Such variants are often large in size, typically 1–5 Mb, but currently available CNV callers have been developed and benchmarked for the discovery of smaller variants. Thus, the ability of these programs to detect tens of real syndromic CNVs remains largely unknown.

Results
Here we present ConanVarvar, a tool which implements a complete workflow for the targeted analysis of large germline CNVs from WGS data. ConanVarvar comes with an intuitive R Shiny graphical user interface and annotates identified variants with information about 56 associated syndromic conditions. We benchmarked ConanVarvar and four other programs on a dataset containing real and simulated syndromic CNVs larger than 1 Mb. In comparison to other tools, ConanVarvar reports 10–30 times less false-positive variants without compromising sensitivity and is quicker to run, especially on large batches of samples.

Conclusions
ConanVarvar is a useful instrument for primary analysis in disease sequencing studies, where large CNVs could be the cause of disease.
petiteFinder: an automated computer vision tool to compute Petite colony frequencies in baker’s yeast
Authors: Nunn Christopher J. , Klyshko Eugene , Goyal Sidhartha 
Published: February 2023

Abstract
Background
Mitochondrial respiration is central to cellular and organismal health in eukaryotes. In baker’s yeast, however, respiration is dispensable under fermentation conditions. Because yeast are tolerant of this mitochondrial dysfunction, yeast are widely used by biologists as a model organism to ask a variety of questions about the integrity of mitochondrial respiration. Fortunately, baker’s yeast also display a visually identifiable Petite colony phenotype that indicates when cells are incapable of respiration. Petite colonies are smaller than their Grande (wild-type) counterparts, and their frequency can be used to infer the integrity of mitochondrial respiration in populations of cells. Unfortunately, the computation of Petite colony frequencies currently relies on laborious manual colony counting methods which limit both experimental throughput and reproducibility.

Results
To address these problems, we introduce a deep learning enabled tool, petiteFinder, that increases the throughput of the Petite frequency assay. This automated computer vision tool detects Grande and Petite colonies and computes Petite colony frequencies from scanned images of Petri dishes. It achieves accuracy comparable to human annotation but at up to 100 times the speed and outperforms semi-supervised Grande/Petite colony classification approaches. Combined with the detailed experimental protocols we provide, we believe this study can serve as a foundation to standardize this assay. Finally, we comment on how Petite colony detection as a computer vision problem highlights ongoing difficulties with small object detection in existing object detection architectures.

Conclusion
Colony detection with petiteFinder results in high accuracy Petite and Grande detection in images in a completely automated fashion. It addresses issues in scalability and reproducibility of the Petite colony assay which currently relies on manual colony counting. By constructing this tool and providing details of experimental conditions, we hope this study will enable larger-scale experiments that rely on Petite colony frequencies to infer mitochondrial function in yeast.
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers
Authors: Zheng Zequn , Song Yongfei 
Published: February 2023

AbstractKCNH2 encodes the human ether-a-go-go-related gene (hERG) potassium channel and is an important repolarization reserve for regulating cardiac electrical activity. Increasing evidence suggests that it is involved in the development of various tumours, yet a thorough analysis of the underlying process has not been performed. Here, we have comprehensively examined the role of KCNH2 in multiple cancers by assessing KCNH2 gene expression, diagnostic and prognostic value, genetic alterations, immune infiltration correlations, RNA modifications, mutations, clinical correlations, interacting proteins, and associated signalling pathways. KCNH2 is differentially expressed in over 30 cancers and has a high diagnostic value for 10 tumours. Survival analysis showed that high expression of KCNH2 was associated with a poor prognosis in glioblastoma multiforme (GBM) and hepatocellular carcinoma (LIHC). Mutations and RNA methylation modifications (especially m6A) of KCNH2 are associated with its expression in multiple tumours. KCNH2 expression is correlated with tumour mutation burden, microsatellite instability, neoantigen load, and mutant-allele tumour heterogeneity. In addition, KCNH2 expression is associated with the tumour immune microenvironment and its immunosuppressive phenotype. KEGG signalling pathway enrichment analysis revealed that KCNH2 and its interacting molecules are involved in a variety of pathways related to carcinogenesis and signal regulation, such as the PI3K/Akt and focal adhesion pathways. Overall, we found that KCNH2 and its interaction molecular are expected to be immune-related biomarkers for cancer diagnosis and prognosis evaluation, and are potential regulatory targets of singalling pathways for tumour development due to their significant role in cancers.
Generalist arbuscular mycorrhizal fungi dominated heavy metal polluted soils at two artisanal and small − scale gold mining sites in southeastern Ecuador
Authors: Suárez Juan Pablo , Herrera Paulo , Kalinhoff Carolina , Vivanco-Galván Oscar , Thangaswamy Selvaraj 
Published: February 2023

Abstract
Background
Artisanal and small-scale gold mining activities are producing contamination with heavy metals and metalloids (HMM) into soils and water worldwide. The HMM are considered as one of the major abiotic stresses due to their long-term persistence in soil. In this context, arbuscular mycorrhizal fungi (AMF) confer resistance to a variety of abiotic plant stressors including HMM. However, little is known regarding the diversity and composition of AMF communities in heavy metal polluted sites in Ecuador.

Methods
In order to investigate the AMF diversity, root samples and associated soil of six plant species were collected from two sites polluted by heavy metals, located in Zamora-Chinchipe province, Ecuador. The AMF 18S nrDNA genetic region was analyzed and sequenced, and fungal OTUs were defined based on 99% sequence similarity. Results were contrasted with AMF communities from a natural forest and from reforestation sites located in the same province and with available sequences in GenBank.

Results
The main pollutants in soils were Pb, Zn, Hg, Cd and Cu with concentrations exceeding the soil reference value for agricultural use. Molecular phylogeny and OTU delimitation showed 19 OTUs, the family Glomeraceae was the most OTU-rich followed by Archaeosporaceae, Acaulosporaceae, Ambisporaceae and Paraglomeraceae. Most of the OTUs (11 of 19) have been found at other locations worldwide, 14 OTUs were proven from nearby non-contaminated sites in Zamora-Chinchipe.

Conclusion
Our study showed that there are no specialized OTUs at the studied HMM polluted sites, but rather generalists adapted to a wide variety of habitats. Their potential role in phytoremediation approaches remains to be investigated.
Detection of neuronal OFF periods as low amplitude neural activity segments
Authors: Harding Christian D. , Guillaumin Mathilde C. C. , Krone Lukas B. , Kahn Martin C. , Blanco-Duque Cristina , Mikutta Christian , Vyazovskiy Vladyslav V. 
Published: February 2023

Abstract
Background
During non-rapid eye movement sleep (NREM), alternating periods of synchronised high (ON period) and low (OFF period) neuronal activity are associated with high amplitude delta band (0.5–4 Hz) oscillations in neocortical electrophysiological signals termed slow waves. As this oscillation is dependent crucially on hyperpolarisation of cortical cells, there is an interest in understanding how neuronal silencing during OFF periods leads to the generation of slow waves and whether this relationship changes between cortical layers. A formal, widely adopted definition of OFF periods is absent, complicating their detection. Here, we grouped segments of high frequency neural activity containing spikes, recorded as multiunit activity from the neocortex of freely behaving mice, on the basis of amplitude and asked whether the population of low amplitude (LA) segments displayed the expected characteristics of OFF periods.

Results
Average LA segment length was comparable to previous reports for OFF periods but varied considerably, from as short as 8 ms to > 1 s. LA segments were longer and occurred more frequently in NREM but shorter LA segments also occurred in half of rapid eye movement sleep (REM) epochs and occasionally during wakefulness. LA segments in all states were associated with a local field potential (LFP) slow wave that increased in amplitude with LA segment duration. We found that LA segments > 50 ms displayed a homeostatic rebound in incidence following sleep deprivation whereas short LA segments (< 50 ms) did not. The temporal organisation of LA segments was more coherent between channels located at a similar cortical depth.

Conclusion
We corroborate previous studies showing neural activity signals contain uniquely identifiable periods of low amplitude with distinct characteristics from the surrounding signal known as OFF periods and attribute the new characteristics of vigilance-state-dependent duration and duration-dependent homeostatic response to this phenomenon. This suggests that ON/OFF periods are currently underdefined and that their appearance is less binary than previously considered, instead representing a continuum.
The proteomics and metabolomics studies of GZU001 on promoting the Merisis of maize (Zea mays L.) roots
Authors: Zheng Zhiguo , Chen Shunhong , Wei Panpan , Guo Shengxin , Yu Gang , Wu Jian 
Published: February 2023

Abstract
Background
Plant growth regulators are chemicals that regulate plant growth and development, which can regulate hormonal balance and affect plant growth, thereby increasing crop yield and improving crop quality. Our studies have revealed a new compound, GZU001, which could be used as a plant growth regulator. This compound has been observed to affect root elongation in maize significantly. However, the exact mechanism of this phenomenon is still being investigated.

Results
Metabolomics and proteomics were used in unison in this study to explore the response pathway and regulation mechanism of GZU001 in promoting maize root elongation. From the appearance, we can see that both roots and plants of maize treated with GZU001 are significantly improved. Maize root metabolism revealed 101 differentially abundant proteins and 79 differentially expressed metabolites. The current study identified altered proteins and metabolites associated with physiological and biochemical processes. GZU001 treatment has been demonstrated to promote primary metabolism, essential for carbohydrates, amino acids, energy, and secondary metabolism. The result suggests that the stimulation of primary metabolism is beneficial for the growth and development of maize and plays a significant role in sustaining metabolism and growth.

Conclusions
This study recorded the changes of related proteins and metabolites in maize roots after GZU001 treatment and provided evidence for this compound’s action mode and mechanism in plants.
Correlation between osteoprotegerin and coronary artery calcification in diabetic subjects: a systematic review of observational studies
Authors: Vazirian Fatemeh , Sadeghi Masoumeh , Wang Dongdong , Javidi Dashtbayaz Reza , Gholoobi Arash , Samadi Sara , Mohammadpour Amir Hooshang 
Published: February 2023

AbstractCoronary artery calcification (CAC) is one of the critical cardiovascular complications that lead to elevated morbidity and mortality among patients with type 2 diabetes (T2M). The association between osteoprotegerin (OPG) and CAC could potentially provide a reasonable chance for preventive therapy in type 2 diabetic patients and benefit the rate of mortality. Since measurement of CAC score is relatively expensive and requires radiation exposure, the current systematic review aims to provide clinical evidence for evaluating the prognostic role of OPG in determining CAC risk among subjects with T2M. Web of Science, PubMed, Embase, and Scopus, were investigated until July 2022. We assessed human studies investigating the association of OPG with CAC in type 2 diabetic patients. Quality assessment was performed by Newcastle–Ottawa quality assessment scales (NOS). Out of 459 records, 7 studies remained eligible to be included. Observational studies that provided odds ratio (OR) estimates with 95% confidence intervals (CIs) for the association between OPG and the risk of CAC were analyzed by random-effects model. In order to provide a visual summary of our findings, the estimation of pooled OR from cross-sectional studies was reported as 2.86 [95% CI 1.49–5.49], which is consistent with the findings of the cohort study. Results revealed that the association between OPG and CAC was significant among diabetic patients. OPG is hypothesized to be a potential marker in predicting the presence of high coronary calcium score among subjects with T2M that could be recognized as a novel target for further pharmacological investigations.
Efficacy of tolvaptan in postoperative volume therapy for acute Stanford type A aortic dissection
Authors: Wang Wenjun , Gao Feng , He Xuezhi , Gao Yang , Shi Lei , Liu Wei , Zhuang Xijing 
Published: February 2023

Abstract
Background
Despite the increasing application of tolvaptan in cardiac surgery, there is no information on the use of tolvaptan in Stanford patients with type A aortic dissection. This study aimed to evaluate the postoperative clinical effects of tolvaptan in patients with type A aortic dissection after tafter surgery.

Methods
A retrospective analysis was performed on 45 patients treated for type A aortic dissection in our hospital from 2018 to 2020. These included 21 patients who were treated with tolvaptan (Group T) and 24 patients who received traditional diuretics (Group L). The hospital's electronic health records were used to obtain perioperative data.

Results
Group T did not differ significantly from Group L in terms of the duration of mechanical ventilation, postoperative blood required, length of catecholamine use, or the amount of intravenous diuretic drugs administered (all P > 0.05). The development of postoperative atrial fibrillation was significantly less in the tolvaptan group (P = 0.023). The urine volumes and change in body weight loss were slightly higher in group T than in group L but the differences were non-significant (P > 0.05). Serum potassium, creatinine, and urea nitrogen levels did not differ between the groups in the week after surgery, At the same time, sodium was significantly higher in the Group T group on day 7 after transfer from the ICU (P = 0.001). In Group L, sodium levels were also elevated by day 7 (P = 0.001). On days 3 and 7, serum creatinine and urea nitrogen levels increased in both groups (both P < 0.05).

Conclusions
Both tolvaptan and traditional diuretics were found to be effective and safe for patients with acute Stanford type A aortic dissection. Moreover, tolvaptan may be associated with reducing the incidence of postoperative atrial fibrillation.
Self efficacy associated with regression from pregnancy-related pelvic girdle pain and low back pain following pregnancy
Authors: Chunmei Dai , Yong Chen , Long Gong , Mingsheng Tan , Hua Li , Ping Yi 
Published: February 2023

Abstract
Background
Self-efficacy, one’s ability to deal with pain, disability, and other symptoms through self-management techniques, positively affect the quality of life in patients with chronic diseases. Pregnancy-related back pain is a common musculoskeletal disorder pre- and postnatally. Hence, the study aimed to determine whether self-efficacy is associated with the development of back pain during pregnancy.

Methods
Between February 2020 and February 2021, a prospective case-control study was performed. Women with back pain were included. The self efficacy was assessed by the Chinese version of the General Self-efficacy Scale (GSES). Pregnancy-related back pain was measured using a self-reported scale. No regression from pregnancy-related back pain is defined as a recurrent or persistent pain score ≥ 3 over a week around 6 months postpartum. Women experiencing back pain during pregnancy are classified according to whether having a regression. This problem can be divided into pregnancy-related low back pain (LBP) and posterior girdle pain (PGP). The differences in variables were compared between groups.

Results
A total of 112 subjects have completed the study finally. These patients were followed up with an average of 7.2 months after childbirth ranging from six to 8 months. 31 subjects (27.7%) of the included women did not report regression 6 months postpartum. The mean self efficacy was 25.2 (SD:10.6). Patients with no regression tended to be older (LBP:25.9 ± 7.2 vs.31.8 ± 7.9, P = 0.023; PGP: 27.2 ± 7.9 vs. 35.9 ± 11.6, P < 0.001*), have a lower self efficacy (LBP:24.2 ± 6.6 vs.17.7 ± 7.1, P = 0.007; PGP: 27.6 ± 6.8 vs. 22.5 ± 7.0, P = 0.010), and need high daily physical demand in their vocations (LBP:17.4% vs. 60.0%, P = 0.019; PGP: 10.3% vs. 43.8%, P = 0.006) when compared to those with regression. Multivariate logistic analysis shows that risk factors for no regression from pregnancy-related back pain included LBP (OR = 2.36, 95%CI = 1.67–5.52, P < 0.001), pain ratings of the onset of back pain during pregnancy≥3(OR = 2.23, 95%CI = 1.56–6.24, P = 0.004), low self efficacy (OR = 2.19, 95%CI = 1.47–6.01, P < 0.001), and high daily physical demand in their vocations (OR = 2.01, 95%CI = 1.25–6.87, P = 0.001).

Conclusions
Low self efficacy makes the women experience about two-fold risk to experience no regression from pregnancy-related back pain. Evaluation for self efficacy is simple enough to be used to improve perinatal health.
Novel fusion protein PK5-RL-Gal-3C inhibits hepatocellular carcinoma via anti-angiogenesis and cytotoxicity
Authors: Gao Xiaoge , Jiang Pin , Wei Xiaohuan , Zhang Wei , Zheng Jiwei , Sun Shishuo , Yao Hong , Liu Xiangye , Zhang Qing 
Published: February 2023

Abstract
Background

Galectin-3 (Gal-3), the only chimeric β-galactosides-binding lectin, consists of Gal-3N (N-terminal regulatory peptide) and Gal-3C (C-terminal carbohydrate-recognition domain). Interestingly, Gal-3C could specifically inhibit endogenous full-length Gal-3 to exhibit anti-tumor activity. Here, we aimed to further improve the anti-tumor activity of Gal-3C via developing novel fusion proteins.

Methods
PK5 (the fifth kringle domain of plasminogen) was introduced to the N-terminus of Gal-3C via rigid linker (RL) to generate novel fusion protein PK5-RL-Gal-3C. Then, we investigated the anti-tumor activity of PK5-RL-Gal-3C in vivo and in vitro by using several experiments, and figured out their molecular mechanisms in anti-angiogenesis and cytotoxicity to hepatocellular carcinoma (HCC).

Results
Our results show that PK5-RL-Gal-3C can inhibit HCC both in vivo and in vitro without obvious toxicity, and also significantly prolong the survival time of tumor-bearing mice. Mechanically, we find that PK5-RL-Gal-3C inhibits angiogenesis and show cytotoxicity to HCC. In detail, HUVEC-related and matrigel plug assays indicate that PK5-RL-Gal-3C plays an important role in inhibiting angiogenesis by regulating HIF1α/VEGF and Ang-2 both in vivo and in vitro. Moreover, PK5-RL-Gal-3C induces cell cycle arrest at G1 phase and apoptosis with inhibition of Cyclin D1, Cyclin D3, CDK4, and Bcl-2, but activation of p27, p21, caspase-3, -8 and -9.

Conclusion
Novel fusion protein PK5-RL-Gal-3C is potent therapeutic agent by inhibiting tumor angiogenesis in HCC and potential antagonist of Gal-3, which provides new strategy for exploring novel antagonist of Gal-3 and promotes their application in clinical treatment.