bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical spectroscopy to characterize protein conformation and conformational changes
Authors: Schmid Franz X 
Published: November 2023

Abstract
Proteins absorb light and emit radiation in the UV range of the spectrum. The absorbance is caused by the peptide groups, by the aromatic amino acids, and to a small extent, by disulfide bonds. Fluorescence emission originates from the aromatic amino acids. Some proteins that carry covalently linked cofactors, such as the haem proteins, also show absorbance in the visible range. Proteins also absorb infrared light. The latter two properties will not be dealt with in this chapter. During absorption, light energy is used to promote electrons from the ground state to an excited state. Electrons that participate in delocalized aromatic systems frequently absorb in the near-UV or the visible region. Fluorescence emission is observed when excited electrons revert from the first excited state to the ground state. When a chromophore is part of an asymmetric structure, or when it is immobilized within an asymmetric environment, left-handed and right-handed circularly-polarized light is absorbed to different extents. This phenomenon is called circular dichroism (CD).
Measuring the conformational stability of a protein
Authors: Pace C Nick , Scholtz J Martin 
Published: November 2023

Abstract
The stability of proteins, especially enzymes, has long been a practical concern (1), because this is usually the factor that most limits their usefulness. There are two very different aspects of protein stability. One is the chemical stability of the covalent structure, which involves covalent changes and is usually irreversible. The other is the conformational stability of the folded state, in the absence of covalent changes (2-8). The latter is the subject of this chapter, which will describe the simplest methods available for measuring how much more stable is the folded conformation of a protein than its unfolded conformations.
Purification of yeast replication origin binding proteins
Authors: Donovan Shane , Dowell Simon , Diffley John , Rowley Adele 
Published: November 2023

Abstract
This chapter provides practical advice on the biochemical purification of proteins that bind to replication origins in the budding yeast Saccharomyces cerevisiae. Genetic and biochemical analysis in budding yeast has facilitated much of our current understanding about the initiation of replication of chromosomal DNA in eukaryotic cells, in large part because only in this organism have the DNA sequences that serve as replication origins been identified and characterized in detail. Replication origins in S. cerevisiae consist of discrete 100--300 bp sequences termed autonomously replicating (ARS) sequences that are both necessary and sufficient for replication of plasmid DNA. At least a subset of ARSs function as origins of replication in their native chromosomal context. The combined power of biochemical and genetic approaches available in yeast has led to the identification of proteins required for initiation of DNA replication that interact, either directly or indirectly, with ARS sequences. Furthermore, recent progress has demonstrated the periodic assembly of complexes involving these proteins at replication origins during the cell cycle and that this process is regulated by cyclin dependent kinases (CDKs). The goal of this chapter is to provide protocols and necessary information for the purification of three origin interacting factors: ORC, Abflp, and Cdc46p, a member of the Mcm family of proteins. Recent evidence also implicates Cdc6p, Dbf4p, and Cdc45p as origin inter acting factors. The characteristics of Cdc6p, Dbf4p, and Cdc45p will be briefly reviewed, however no protocols are yet available for the purification of these proteins from yeast. For more comprehensive discussion of ARS sequence characteristics, ARS binding proteins, and cell cycle regulation of initiation the reader is directed to a number of recent reviews (1-6).
Biotilms in the brewing process - a new approach to hygiene management
Authors: Storgards E , Pihlajamaki O , Haikara A 
Published: November 2023

Abstract
Detection and removal of surface contaminants are still poorly optimized. Biofilm formation was studied in order to facilitate the elimination and prevention of biofouling on the basis of accurate data. Epifluorescence microscopy, ATP bioluminescence measurements and traditional cultivation were used for studying microbial growth on stainless steel surfaces. Biofilm formation was also studied in immobilized yeast reactors used for continuous secondary fermentation. Acetobacter sp, Gluconobacter oxydans, L. lindneri, Pantoea agglomerans, Dekkera anomala (anam. Brettanomyces anomalus) and Saccharomyces cerevisiae (ex. diastaticus) were strong biofilm producers. Attachment of L. lindneri to yeast cells and carrier materials in immobilized yeast reactors was intense.
Cell polarity in ciliates
Authors: Frankel Joseph 
Published: November 2023

Abstract
As pointed by Wolpert (1), the term ‘polarity’ is used by biologists in two different senses (Fig. 1). One is the expression of different spatially segregated qualities or attributes. These might characterize the opposite ends of a system, such as the budding and non-budding poles of a yeast cell (2), or else they might partition the entire system into two relatively homogeneous regions, such as the apical and basolateral domains of an epithelial cell (3). I will call this domain polarity. The other sense embodies the notion of a direction, or vector, that pervades the entire system. It is this latter sense that Crick had in mind when he stated that’a system of polarities … necessarily implies a vector field’ (4, p. 436). I will call this vectorial polarity.
Hybridization At Oligonucleotid Sensitive Electrodes
Authors: Caruana Daren J 
Published: November 2023

Abstract
DNA hybridization on solid surfaces was developed on membranes as a routine biotechnological technique in the 1970s (1). With the invention and refinement of new surface analytical techniques, oligonucleotide detection by surface con-fined hybridization is the fundamental principle behind the function of most oligonucleotide sensitive devices. These devices are capable of high throughput DNA analysis for applications such as sequencing, genetic diagnosis, drug phenotyping, computing, and gene expression analysis.
Genetic Association Between ICAM-1 Gene Variants and Susceptibility to Ischemic Cardiomyopathy
Authors: Naman Tuersunjiang , Abuduhalike Refukaiti , Abudouwayiti Aihaidan , Abudurexiti Muyashaer , Sun Juan , Mahemuti Ailiman 
Published: November 2023

Abstract:
The current work was aimed at exploring the association between single nucleotide polymorphisms (SNPs) in the ICAM-1 gene, along with the identification of additional haplotypes and their potential role in the susceptibility to ischemic cardiomyopathy (ICM). The control group underwent a Hardy–Weinberg equilibrium test. The associations of genotypes and alleles with susceptibility to ICM were then analyzed using logistic regression analysis. Subsequently odds ratios (ORs) along with 95% confidence intervals (95% CI) were calculated. Interaction analysis was conducted between these SNPs. Furthermore, linkage disequilibrium analysis and haplotype analysis were performed on SNPs that showed interactions with each other. The incidence of ICM was significantly higher among individuals carrying the T allele of rs3093032 (OR = 2.032, 95% CI, 1.275–3.241, P = 0.003) relative to those with the C allele. In addition, CT genotype carriers had a higher susceptibility to ICM than CC genotype carriers (OR = 2.490, 95% CI, 1.445–4.29, P = 0.001). Furthermore, 3 SNPs (rs3093032, rs923366, rs3093030) exhibited a strong interaction with each other, whereas rs281437 showed no interaction with the other 3 SNPs. Individuals carrying the Crs3093032-Trs923366-Crs3093030 haplotype had an elevated risk of ICM compared with those carrying the Crs3093032-Crs923366-Crs3093030 haplotype (OR = 2.280, 95% CI, 1.568–3.315, P < 0.001). Moreover, individuals carrying the Trs3093032-Crs923366-Crs3093030 haplotype were more susceptible to ICM than those carrying the Crs3093032-Crs923366-Crs3093030 haplotype (OR = 2.388, 95% CI, 1.469–3.880, P < 0.001). Regarding rs3093032, the minor alleles and haplotypes are associated with an increased ICM risk: 3 SNPs (rs3093032, rs923366, rs3093030) in ICAM-1 have strong interaction with each other.
Prevalence and long-term implications of preoperative anemia in patients undergoing elective general surgery – a retrospective cohort study at a university hospital
Authors: Braunschmid Tamara , Graf Alexandra , Eigenbauer Ernst , Schak Gerhard , Sahora Klaus , Baron David M. 
Published: November 2023

Objective:
The aim of this retrospective study was to assess the prevalence of anemia in a cohort of patients undergoing elective general surgery at a university hospital. Furthermore, we investigated the influence of anemia on short-term and long-term postoperative outcome.

Background:
Awareness of the negative impact of preoperative anemia on perioperative morbidity and mortality is rising. Anemia is a potentially modifiable factor, and its therapy might improve patient outcome in elective surgery. Nevertheless, patients with preoperative anemia frequently undergo elective surgery without receiving adequate preoperative treatment.

Methods:
In this single-center cohort study, we analyzed 6908 adult patients who underwent elective general surgery. Patients undergoing day-clinic surgery were excluded. In all patients, preoperative hemoglobin (Hb) concentration and hematocrit (Hct) was available.

Results:
Of all patients analyzed, 32.9% were anemic (21.0% mild, 11.8% moderate, 1.1% severe). Median time to last follow up was 5.2 years. During the whole study period, 27.1% of patients died (1.2% died during the hospital stay); median time to death was 1.3 years. Patients with preoperative anemia had significantly higher mortality rates (P<0.001) and a higher probability of postoperative complications (P<0.001). Likewise, receiving blood transfusions was associated with a higher risk of death (P<0.001).

Conclusion:
This retrospective single-center analysis confirmed that preoperative anemia is common, and is a significant risk factor for unfavorable postoperative outcome. As anemia is a modifiable risk factor, the implementation of a PBM concept is crucial to reduce detrimental postoperative events associated with anemia.
Non-invasive prediction of perineural invasion in intrahepatic cholangiocarcinoma by clinicoradiological features and computed tomography radiomics based on interpretable machine learning: a multicenter cohort study
Authors: Liu Ziwei , Luo Chun , Chen Xinjie , Feng Yanqiu , Feng Jieying , Zhang Rong , Ouyang Fusheng , Li Xiaohong , Tan Zhilin , Deng Lingda , Chen Yifan , Cai Zhiping , Zhang Ximing , Liu Jiehong , Liu Wei , Guo Baoliang , Hu Qiugen 
Published: November 2023

Background:
Perineural invasion (PNI) of intrahepatic cholangiocarcinoma (ICC) is a strong independent risk factor for tumor recurrence and long-term patient survival. However, there is a lack of non-invasive tools for accurately predicting the PNI status. We develop and validate a combined model incorporating radiomics signature and clinicoradiological features based on machine learning for predicting PNI in ICC, and used the Shapley Additive explanation (SHAP) to visualize the prediction process for clinical application.

Methods:
This retrospective and prospective study included 243 patients with pathologically diagnosed ICC (training, n=136; external validation, n=81; prospective, n=26, respectively) who underwent preoperative contrast-enhanced CT between January 2012 and May 2023 at three institutions (three tertiary referral centers in Guangdong Province, China). The ElasticNet was applied to select radiomics features and construct signature derived from CT images, and univariate and multivariate analyses by logistic regression were used to identify the significant clinical and radiological variables with PNI. A robust combined model incorporating radiomics signature and clinicoradiological features based on machine learning was developed and the SHAP was used to visualize the prediction process. A Kaplan–Meier survival analysis was performed to compare prognostic differences between PNI positive and negative groups and was conducted to explore the prognostic information of the combined model.

Results:
Among 243 patients (mean age, 61.2 y ± 11.0 (SD); 152 men and 91 women), 108 (44.4%) were diagnosed as PNI-positive. The radiomics signature was constructed by seven radiomics features, with areas under the curves (AUCs) of 0.792, 0.748, and 0.729 in the training, external validation, and prospective cohorts, respectively. Three significant clinicoradiological features were selected and combined with radiomics signature to construct a combined model using machine learning. The eXtreme Gradient Boosting (XGBoost) exhibited improved accuracy and robustness (AUCs of 0.884, 0.831, and 0.831, respectively). Survival analysis showed the construction combined model could be used to stratify relapse-free survival (hazard ratio, 1.933; 95% confidence interval (CI): 1.093–3.418; P=0.021).

Conclusions:
We developed and validated a robust combined model incorporating radiomics signature and clinicoradiological features based on machine learning to accurately identify the PNI statuses of ICC, and visualize the prediction process through SHAP for clinical application.
The Medical Impact of Emergent Banning of N-nitrosodimethylamine (NDMA)- contaminated Antihypertensive Drug: A nationwide longitudinal cohort study
Authors: Ahn Juhee , Won Sungho , Park Jong-Heon , Shimbo Daichi , Lee Hae-Young 
Published: November 2023

AbstractOBJECTIVETo study the association of NDMA-contaminated generic valsartan with cancer incidence.DESIGNNationwide longitudinal observational cohort study.SETTINGClaims data from the National Health Insurance Service of South Korea was analyzed using 1:1:1 pairwise propensity score matching (PSM) of NDMA-uncontaminated original, NDMA-contaminated generic, and initially-suspended-but-finally confirmed as NDMA-uncontaminated generic valsartan user-groups. Time-dependent Cox models and dose- response evaluation were used to evaluate carcinogenicity.PARTICIPANTSA total of 3,231,212 participants with satisfactory minimal adherence, followed up from January 1, 2013 until December 31, 2020.INTERVENTIONSAt least one tablet of valsartan.MAIN OUTCOME MEASURESThe primary outcome was primary cancer incidence and secondary outcome was 12 prevalent organ-specific cancer incidences. All-cause and cardiovascular mortality risks were estimated before and after valsartan withdrawal.RESULTSAmong participants (mean [standard deviation] age 59.5 [13.1] years; male, 53.5%), new users had adjusted hazard ratios and 95% confidence intervals (CI) of 1.069 (1.054 to 1.085) and 1.142 (1.100 to 1.186) for any cancer in the NDMA-exposed period (versus NDMA-unexposed) before and after 1:1:1 PSM, respectively. Regardless of PSM, lung and prostate cancer risks increased significantly during the NDMA-exposed period whereas, post-PSM, cancer risk did not increase in the eventually-NDMA-uncontaminated group, even in new users. All-cause and cardiovascular mortality did not differ significantly with NDMA exposure before and after emergent banning.CONCLUSIONSNDMA-contaminated valsartan increased cancer risk, especially of lung and prostate cancers. All-cause and cardiovascular mortality did not evidently increase following banning. This supports emergent health-policy action against potentially carcinogenic drugs.
ntsm: an alignment-free, ultra low coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection
Authors: Chu Justin , Rong Jiazhen , Feng Xiaowen , Li Heng 
Published: November 2023

AbstractBackgroundDue to human error, sample swapping in large cohort studies with heterogeneous data types (e.g. mix of Oxford Nanopore, Pacific Bioscience, Illumina data,etc.) remains a common issue plaguing large-scale studies. At present, all sample swapping detection methods require costly and unnecessary (e.g. if data is only used for genome assembly) alignment, positional sorting, and indexing of the data in order to compare similarly. As studies include more samples and new sequencing data types, robust quality control tools will become increasingly important.FindingsThe similarity between samples can be determined using indexedk-mer sequence variants. To increase statistical power, we use coverage information on variant sites, calculating similarity using a likelihood ratio-based test. Per sample error rate, and coverage bias (i.e. missing sites) can also be estimated with this information, which can be used to determine if a spatially indexed PCA-based pre-screening method can be used, which can greatly speed up analysis by preventing exhaustive all-to-all comparisons.ConclusionsBecause this tool processes raw data, is faster than alignment, and can be used on very low coverage data, it can save an immense degree of computational resources in standard QC pipelines. It is robust enough to be used on different sequencing data types, important in studies that leverage the strengths of different sequencing technologies. In addition to its primary use case of sample-swap detection, this method provides other useful information useful in QC, such as error rate and coverage bias, as well as population-level PCA ancestry analysis visualization.
Drivers of phenotypic differentiation across rock outcrop sky islands inImpatiensplants
Authors: Rahim Sumayya Abdul , Kulkarni Aboli , Kodandaramaiah Ullasa 
Published: November 2023

AbstractHabitat specialization can lead to naturally fragmented populations separated by unoccupied habitats that comprise potential barriers to dispersal. Habitat fragmentation can result in phenotypic divergence between populations, and eventual speciation. We investigate trait divergence in a habitat specialist plant species –Impatiens lawii– that is specialized on rock outcrops in the Western Ghats mountains of India. We compare trait divergence in this species with that in a closely related species,I. oppositifolia, which is a continuously distributed habitat generalist that co-occurs with the former species on rock outcrops in addition to being found in intervening regions. As predicted, we found that floral traits were more strongly structured across populations inI. lawiithan inI. oppositifolia, supporting the role of habitat specialization. In both species, floral traits were more strongly structured across populations than were vegetative traits. Interestingly, the population pairs that were significantly differentiated for floral traits differed from those differentiated for vegetative traits. Furthermore, some population pairs differed in vegetative traits but not in floral traits. The incongruence in patterns of floral and vegetative trait differentiation suggests the role of selection. There was no association between floral trait variation and geographic distance in either species. Surprisingly, there was a significant correlation between geographic distance and vegetative trait variation inI. oppositifolia, but not inI. lawii(Fig 4D; Table 2), possibly due to genetic drift. Overall, a combination of habitat specificity, drift and selection best explains trait variation inI. lawii.
Allometry of cell types in planarians by single cell transcriptomics
Authors: Emili Elena , Pérez-Posada Alberto , Christodoulou Maria D. , Solana Jordi 
Published: November 2023

AbstractAllometry explores the relationship between an organism’s body size and its various components, offering insights into ecology, physiology, metabolism, and disease. The cell is the basic unit of biological systems, and yet, the study of cell type allometry remains relatively unexplored. Single-cell RNA sequencing (scRNA-seq) provides a promising tool for investigating cell type allometry. Planarians, capable of growing and degrowing following allometric scaling rules, serve as an excellent model for such studies. We used scRNA-seq to examine cell type allometry in asexual planarians of different sizes, revealing that they consist of the same basic cell types but in varying proportions. Notably, the gut basal cells are the most responsive to changes in size, suggesting a role in energy storage. We capture the gene regulatory programs of distinct cell types in response to size. This research sheds light on the molecular and cellular aspects of cell type allometry in planarians and underscores the utility of scRNA-seq in such investigations.
Anin vivoplatform to identify pathogenic loci
Authors: Yamada Shigehiro , Ou Tiffany , Nachadalingam Sibani ,   PreMIER Consortium, Yang Shuo , Johnson Aaron N. 
Published: November 2023

SummaryRare genetic disease discovery efforts typically lead to the identification of new disease genes. PreMIER (PrecisionMedicine IntegratedExperimentalResources) is a collaborative platform designed to facilitate functional evaluation of human genetic variants in model systems, and to date the PreMIER Consortium has evaluated over 50 variants in patients with genetic disorders. To understand ifDrosophilacould be used to identify pathogenic disease loci as part of the PreMIER Consortium, we used tissue-specific gene knockdown in the fly as a proof of principle experiment. Tissue-specific knockdown of seven conserved disease genes caused significant changes in viability, longevity, behavior, motor function, and neuronal survival arguing a set of defined assays can be used to determine if a gene of uncertain significance (GUS) regulates specific physiological processes. This study highlights the utility of a tissue-specific knockdown platform inDrosophilato characterize GUS, which may provide the first genephenotype correlations for patients with idiopathic genetic disorders