bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation of subcellular fractions
Authors: Hinton Richard H , Mullock Barbara M 
Published: November 2023

Abstract
The aim of subcellular fractionation is to separate cell organelles with as little damage as possible. The first thing to remember is that it will never be possible to separate organelles completely undamaged. In the living cell, most of the cell organelles are attached to cytoskeletal elements and are surrounded by cytosol which is a 20% solution of protein in which most of the water is bound to the hydration sphere of the proteins. Breakage of the linkage to the cytoskeleton and alterations in the environment will thus inevitably result in alterations to the cell organelles and these alterations will undoubtedly be exacerbated by damage occurring during homogenization, as discussed in Chapter 1, and damage occurring during the course of separation, as discussed in this and subsequent chapters. Thus it will never be possible to separate cell organelles in a completely natural state and, in fact, there is never a single best way to fractionate a tissue. For example, the method used to determine the distribution of some material between cell organelles may differ markedly from the method used to isolate a particular organelle with the minimum of damage. The first aim of this chapter will be to discuss the general principles of both analytical and preparative methods for cell fractionation.
Mutation detection and diagnosis Using PFGE
Authors: Dunnen J T Den , Liang P , Van Ommen, G J B , Van Broeckhoven C 
Published: November 2023

Abstract
Pulse field gel electrophoresis (PFGE) was specifically designed to separate large DNA fragments (1). Consequently, the great innovation of PFGE analysis for mutation identification and diagnosis was its range of detection and its ability to scan for genetic rearrangements at large distances from a given locus (probe). For a specific disease, when closely linked genetic markers become available, PFGE analysis is used to determine the physical map of the region involved. Simultaneous analysis of patient material will quickly reveal if large chromosomal aberrations play a role in the development of the disease. In the case of Duchenne muscular dystrophy (DMD) this has led to the detection of large deletions and duplications as the diseasecausing mutation in over 50% of the patients at a time when the gene involved had not yet been identified (2). Similarly, PFGE allowed the detection of large chromosomal duplications in a majority of patients with Charcot-Marie-Tooth disease type la (CMTla), with probes that had been shown to be closely linked by genetic mapping (3, 4). Again, at that time, the responsible gene(s) had not yet been identified.
Footprint analysis of DNA—protein complex.es i.n vitro and lil VlVO
Authors: Spiro Craig , Y Cynthia T Mcmurra 
Published: November 2023

Abstract
Protein-DNA complexes mediate essential processes such as transcription and DNA replication. Footprint experiments use chemicals and enzymes that modify DNA to obtain detailed information on the individual nucleotides in protein-DNA complexes, even inside living mammalian cells.
Reverse genetics of RNA viruses
Authors: Bridgen A , Elliott R M 
Published: November 2023

Abstract
RNA viruses comprise many of the most serious human pathogens. There are now possibly 500 million carriers of hepatitis C virus world-wide (1). Rotavirus infections are responsible for around 18 million cases of severe diarrhoea and nearly 1 million deaths in young children in developing countries annually (2). Measles is still also one of the leading causes of infant death in developing countries, and can induce the rare, but fatal, neurodegenerative disease subacute sclerosing panencephalitis (3). Many human respiratoiy infections are caused by RNA viruses such as influenza, human respiratoiy syncytial virus, coronaviruses, enteroviruses and, one of the most frequent virus pathogens of humans, the rhinoviruses (4). Hantaviruses, members of the Bunyaviridae family, are responsible for haemorrhagic diseases and form one of a number of virus groups whose incidence has increased greatly over the last few years, the so-called ‘emerging viruses’ (5). Perhaps the most frightening of all virus diseases, because of their high mortality and lack of effective prophylaxis and treatment, are those caused by the filoviruses Marburg and Ebola (6).
Molecular modelling
Authors: Kroemer Romano T 
Published: November 2023

Abstract
Molecular modelling or computational chemistry have come a long way. From the era when they were restricted to a small number of scientists using very specialized and user-unfriendly software/hardware to the present where we are confronted with a vast amount of well integrated programs and relatively cheap hardware. The recent explosion of the Internet has added significantly to the amount of software available, as it is often accessible directly via the net. Now-adays, many of these programs can be used also by someone without programming expertise, and it is not necessary to have studied theoretical chemistry for years beforehand. However, the program in question should not be treated as a black box either and the user must have an understanding of the underlying theory and concepts.
Evaluating receptor stoichiometry by fluorescence resonance energy transfer
Authors: Gakamsky Dmitry M , Pecht Israel 
Published: November 2023

Abstract
Elucidating mechanisms of molecular interactions among receptors and their ligands is a central problem in cell and molecular biology. Many different methods, including gel filtration, radiolabelling, immunoprecipitation, two-hybrid system analysis, circular dichroism, fluorescence and absorption spectroscopy, and surface plasmon resonance, have been developed to reveal the proximity of proteins in cells, their organization into molecular complexes, and to determine their stoichiometry. The present review focuses on the use of fluorescence resonance energy transfer (FRET), which is a universal, versatile, and powerful approach for evaluating/assaying distances between and within molecules. In comparison with other methods, FRET has numerous advantages. The exquisite sensitivity provided by a fluorescence detection method (single molecule detection is possible), coupled with the wide range of fluorescence-based instrumentation (e.g. microscopy, flow cytometry, steady-state fluorimetry, fluorescence polarization, fluorescence lifetime, rapid mixing devices) and a large variety of commercially available fluorescent probes, allows numerous possible approaches for studying biological structure and function. Moreover, the ability to measure the concentration of bound complexes, without the need to separate them from the unbound fraction, together with the potential for high spatial resolution, make FRET an excellent tool for the study ofreal time receptor-ligand interactions in individual cells (1-3). This is illustrated by the recent application of FRET to the design of high throughput screening instruments in drug design (4, 5). In this chapter we describe FRET applications in the determination of complex molecular organization and stoichiometry in solutions and in living cells.
Monitoring intracellular trafficking of receptors
Authors: Molloy Raymond , Hughes Thomas E , Robert Antoine , Howe James R 
Published: November 2023

Abstract
When appended to a membrane protein as a genetic fusion, the green fluorescent protein (GFP) can be used to mark both the presence and amount of receptor in the cellular compartments ofliving cells (1). The great advantage of this approach is that it affords a unique view of protein trafficking as it occurs. Fluorescent receptors can therefore serve as direct assays for the determinants of protein dynamics. Indeed, the creative ferment that has developed as researchers continue to devise new approaches is one of the main attractions of this emerging field.
It is helpful to begin by understanding why the GFP is so useful as well as some of the disadvantages. The protein comprises 238 amino acids and adopts a unique barrel-shaped structure (2) whose 11 staves in the beta sheet conformation surround the fluorophore. One drawback to using GFP as a tag, then, is simply the large size of the protein. Fortunately, its remarkably compact and self-contained structure appears, empirically, to minimize interactions with neighbouring proteins. In addition, both the N- and C-termini extend from the same end of the barrel so that, despite its size, the GFP can be placed within another coding sequence without adding much physical distance between the two parts of the receptor.
Regulation of receptors and receptor-coupled ion channels by protein phosphorylation
Authors: McDonald Bernard J , Huganir Richard L 
Published: November 2023

Abstract
Phosphorylation of serine, threonine, or tyrosine residues is accepted to be a key mechanism for the regulation of protein structure and function in the cellular environment. This highly dynamic process is catalysed by a diverse group of enzymes termed protein kinases (1) and is reversed by another group called phosphatases (2). Phosphorylation status has been shown to regulate the function, distribution, and interactions of numerous classes of proteins including those involved in transmembrane signalling, cytoskeletal dynamics, cell division, and transcriptional regulation (3-6). The importance of protein phosphorylation in the transduction of extracellular stimuli and the generation of appropriate cellular responses is well established. Such responses depend critically on the correct phosphorylation of a multitude of proteins in response to signals arriving at the plasma membrane; for example hormones, growth factors, neurotransmitters, and alterations in membrane potential. Given the diversity of such stimuli and the complexity of the responses they elicit throughout the cell, it is crucial that the initial response at the plasma membrane is tightly regulated.
Combined Bilateral Salpingo-oophorectomy and Cesarean Delivery in BRCA1/2 Alteration Carriers
Authors: Barker Victoria E. , Vlachodimitropoulou Evangelia , O’Brien Patrick , Iskaros Joseph , Rosenthal Adam N. 
Published: November 2023

BACKGROUND:
The cumulative lifetime risk of ovarian cancer is 16–68% and 11–30% in female BRCA1 and BRCA2 gene alteration carriers, respectively. Risk-reducing bilateral salpingo-oophorectomy (RRSO) is the only proven way to reduce ovarian cancer mortality. We report a series of patients who underwent risk-reducing surgery at the time of planned obstetric-indicated cesarean delivery.

CASES:
This is a case series of four women carrying a pathogenic germline BRCA1 or BRCA2 gene alteration who underwent RRSO at the time of cesarean delivery between March 1, 2018, and March 31, 2022. All women were referred during pregnancy to the University College London Hospitals Familial Cancer Clinic for consideration of RRSO at the time of obstetric-indicated cesarean delivery. Women were considered eligible for RRSO if they had a proven pathogenic germline alteration, would have completed childbearing after the cesarean delivery, and were older than age 35 or 40 years with BRCA1 or BRCA2 alterations, respectively. Operating time, blood loss, transfusion requirements, length of hospital stay, complications, and ability to breastfeed were assessed and, where possible, compared with the institutional means for similar patients who underwent cesarean delivery only, to determine whether RRSO was associated with increased morbidity. Women were contacted 11–59 months postprocedure to assess satisfaction. The mean blood loss was 687 mL (range 400–1,000 mL), mean operating time was 68 minutes, mean length of hospital stay was 3 days, and mean change in hemoglobin was −1 g/dL. No patient required a transfusion, had internal organ damage, returned to the operating room, or was readmitted. One of two women with intact breast tissue successfully breastfed, and the other chose to bottle feed. The mean contemporaneous institutional blood loss for cesarean delivery was not significantly different at 681 mL for singleton pregnancies and 872 mL for twin pregnancies. All four women reported a high level of satisfaction with the combined procedure.

CONCLUSION:
Our results show that RRSO can be performed at the time of cesarean delivery with high patient satisfaction. This approach can be offered to appropriately counseled individuals, with the benefit of avoiding the need for two separate procedures, with potentially reduced patient morbidity and health care costs.
Comparison of Morbidity and Retreatment After Urethral Bulking or Midurethral Sling at the Time of Pelvic Organ Prolapse Repair
Authors: Russell Rebekah , Rhodes Stephen , Gupta Ankita , Bretschneider C. Emi , Ferrando Cecile A. , Hijaz Adonis , Shoag Jonathan , Sheyn David 
Published: November 2023

OBJECTIVE:
To compare postprocedure retreatment rates for stress incontinence in patients who underwent either midurethral sling or urethral bulking at the time of concomitant repair of pelvic organ prolapse (POP).

METHODS:
This was a retrospective cohort study using data from the Premier Healthcare Database. Using Current Procedural Terminology codes, we identified patients who were undergoing POP repair and concomitant urethral bulking or midurethral sling between the years 2001 and 2018. Patients who underwent concomitant nongynecologic surgery, Burch urethropexy, or oncologic surgery, and those who did not undergo concomitant POP and anti-incontinence surgery, were excluded. Additional data collected included patient demographics, hospital characteristics, surgeon volume, and comorbidities. The primary outcome was a repeat anti-incontinence procedure at 2 years, and the secondary outcome was the composite complication rate.

RESULTS:
Over the study period, 540 (0.59%) patients underwent urethral bulking, and 91,005 (99.41%) patients underwent midurethral sling. The rate of a second procedure within 2 years was higher for urethral bulking, compared with midurethral sling (9.07% vs 1.11%, P<.001); in the urethral bulking group, 4.81% underwent repeat urethral bulking and 4.81% underwent midurethral sling. In the midurethral sling group, 0.77% underwent repeat midurethral sling and 0.36% underwent urethral bulking. After adjusting for confounders, midurethral sling was associated with a decreased odds of a repeat anti-incontinence procedure at 2 years (adjusted odds ratio 0.11, 95% CI 0.08–0.16). The probability of any complication at 2 years was higher with urethral bulking (23.0% vs 15.0%, P<.001).

CONCLUSION:
Urethral bulking at the time of POP repair is associated with a higher rate of repeat procedure and postoperative morbidity up to 2 years after surgery.
Association between cerebrovascular disease and perioperative neurocognitive disorders: a retrospective cohort study
Authors: Feng Lan , Liu Yuanhui , Li PengFei , Wan Hengjun , Deng Xiren , Wang Tingting , Fu Hong , Duan Xiaoxia 
Published: November 2023

Background:
Previous studies have shown that patients with cerebrovascular disease (CVD) have a significantly increased risk of cognitive decline or dementia; however, the association between preoperative CVD and perioperative neurocognitive disorders (PNDs) remains unclear. This study aimed to explore the correlation between preoperative CVD and PNDs, as well as combine logistic regression and ROC curves to construct a clinical prediction PND model.

Materials and Methods:
This retrospective cohort study evaluated 13,899 surgical patients of a large-scale comprehensive hospital between January 2021 and January 2022 to explore the association between preoperative CVD and PNDs, with follow-up to monitor postoperative survival until February 28, 2023, unless the patient died. The study participants comprised all inpatients from the Bone and Joint Surgery, Spine Surgery, Urology, Hepatobiliary Surgery, Gastrointestinal Surgery, and Thoracic Surgery departments. Patients were classified into two groups: the CVD group with a confirmed diagnosis and the non-cerebrovascular disease (NCVD) group. The incidence of PNDs was measured, and potential associations between patient demographic information, preoperative comorbidities, and CVD, as well as the correlation between preoperative CVD and PNDs, were investigated by multivariate logistic regression analysis. Next, we constructed a clinical prediction PND model by drawing the receiver operating characteristic (ROC) curve. The postoperative survival of all patients was tracked, and a survival curve was constructed and incorporated into the Cox proportional hazard regression model to analyze the relationship between preoperative CVD and overall postoperative survival rate.

Results:
Of the included 13,899 patients, propensity score matching yielded 1006 patient pairs. Multivariate logistic regression analysis revealed that CVD was an independent risk factor for PNDs [Odds ratio: 10.193; 95% confidence interval: 7.454–13.938; P<0.001]. Subsequently, we developed a clinical prediction model for PNDs by multivariate logistic regression analysis. The area under the ROC curve was 0.798 (95% CI: 0.765–0.830). The survival of 11,702 patients was followed up. Multivariate Cox hazard ratio regression analysis revealed that CVD affected the overall postoperative survival rate (Hazard ratio, 1.398; 95% confidence interval: 1.112–1.758; P＜0.001).

Conclusion:
CVD was an independent risk factor for PNDs and affected the overall postoperative survival rate of surgical patients with preoperative CVD.
Timing of restoration of bowel continuity after decompressing stoma, in left-sided obstructive colon cancer – A nationwide retrospective cohort
Authors: Zamaray Bobby , Veld Joyce V. , Brohet Richard , Consten Esther C.J. , Tanis Pieter J. , van Westreenen Erik L. ,   on behalf of the Dutch Snapshot Research Group and the Dutch Complex Colon Cancer Initiative (DCCCI)
Published: November 2023

Background:
With increasing use of decompressing stoma as bridge to surgery for left-sided obstructive colon cancer, timing of restoration of bowel continuity (ROBC) is a subject of debate. There is a lack of data on immediate ROBC during elective resection as alternative for a 3-stage procedure. This study analysed if immediate ROBC during tumour resection is safe and of any benefit for patients who underwent decompressing stoma for left-sided obstructive colon cancer.

Methods:
In a Dutch nationwide collaborative research project, 3153 patients who underwent resection for left-sided obstructive colon cancer in 75 hospitals (2009-2016) were identified. Extensive data on disease and procedural characteristics, and outcomes was collected by local collaborators. For this analysis, 332 patients who underwent decompressing stoma followed by curative resection were selected. Immediate ROBC during tumour resection was compared to two no immediate ROBC groups, (1) tumour resection with primary anastomosis (PA) with leaving the decompressing stoma in situ, and (2) tumour resection without PA.

Results:
Immediate ROBC was performed in 113 patients (34.0%) and no immediate ROBC in 219 patients (168 with PA (50.6%) and 51 patients without PA (15.4%)). No differences at baseline between the groups were found for age, ASA score, cT and cM. Major surgical complications (8.8% immediate ROBC vs. 4.8% PA with decompressing stoma and 7.8% no PA; P=0.37) and mortality (2.7% vs. 2.4% and 0%, respectively; P=0.52) were similar. Immediate ROBC resulted in a shorter time with a stoma (mean 41 vs. 240 and 314 days, respectively; P<0.001), and fewer permanent stomas (7% vs. 21% and 80%, respectively; P<0.001) as compared to PA with decompressing stoma or no PA.

Conclusion:
After decompressing stoma for left-sided obstructive colon cancer, immediate ROBC during elective resection appears safe, reduces the total time with a stoma and the risk of a permanent stoma.
Serum Humanin in Pediatric Septic Shock Associated Multiple Organ Dysfunction Syndrome
Authors: Atreya Mihir R. , Piraino Giovanna , Cvijanovich Natalie Z. , Fitzgerald Julie C. , Weiss Scott L. , Bigham Michael T. , Jain Parag N. , Schwarz Adam J. , Lutfi Riad , Nowak Jeffrey , Thomas Neal J. , Baines Torrey , Haileselassie Bereketeab , Zingarelli Basilia 
Published: November 2023

AbstractBackgroundMultiple organ dysfunction syndrome (MODS) disproportionately contributes to pediatric sepsis morbidity. Humanin (HN) is a small peptide encoded by mitochondrial DNA and thought to exert cytoprotective effects in endothelial cells and platelets. We sought to test the association between serum HN (sHN) concentrations and MODS in a prospectively enrolled cohort of pediatric septic shock.MethodsHuman MT-RNR2 ELISA was used to determine sHN concentrations on day 1 and 3. The primary outcome was thrombocytopenia associated multi-organ failure (TAMOF). Secondary outcomes included individual organ dysfunctions on day 7. Associations across pediatric sepsis biomarker (PERSEVERE) based mortality risk strata and correlation with platelet and markers endothelial activation were tested.Results140 subjects were included in this cohort, of whom 39 had TAMOF. The concentration of sHN was higher on day 1 relative to day 3, and among those with TAMOF phenotype in comparison to those without. However, the association between sHN and TAMOF phenotype was not significant after adjusting for age and illness severity in multivariate models. In secondary analyses, sHN was associated with presence of day 7 sepsis-associated acute kidney injury (SA-AKI) (p = 0.049). Further, sHN was higher among those with high PERSEVERE-mortality risk strata and correlated with platelet counts and several markers of endothelial activation.ConclusionFuture investigation is necessary to validate the association between sHN and SA-AKI among children with septic shock. Further, mechanistic studies that elucidate the role of humanin may lead to therapies that promote organ recovery through restoration of mitochondrial homeostasis among those critically ill.
Jiella pelagia sp. nov., isolated from the phosphonate-amended seawater of the northwestern Pacific Ocean
Authors: Shin Dong Young , Hong Yeon Woo , Kim Soo Yoon , Choi Jy Young , Kim Bok Jin , Kang Jin Kyeong , Cho Byung Cheol , Hwang Chung Yeon 
Published: November 2023

A novel Gram-stain-negative, aerobic, rod-shaped bacterium, designated as HL-NP1T, was isolated from the surface water of the northwestern Pacific Ocean after enrichment cultivation using the organic phosphorous compound of 2-aminoethylphosphonate. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus

Jiella

, with the highest similarity to

Jiella pacifica

40Bstr34T (98.7 %). The complete genome sequence of strain HL-NP1T comprised a circular chromosome of 5.58 Mbp and two circular plasmids of 0.15 and 0.22 Mbp. Comparison of the genome sequences between strains HL-NP1T and

J. pacifica

40Bstr34T revealed that average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values (88.0, 86.4 and 33.9 %, respectively) were below the recommended cut-off levels for delineating bacterial species. Strain HL-NP1T showed optimal growth at 30 °C, pH 6.5–7.0, with 2.0–2.5 % (w/v) NaCl. The sole respiratory quinone was ubiquinone-10. The predominant fatty acid was summed feature 8 (C18 : 1
ω6c and/or C18 : 1
ω7c). The polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, an unidentified aminolipid and four unidentified lipids. The G+C content of the genomic DNA was 65.1 %. Based on phylogenetic, genotypic, phenotypic and chemotaxonomic data, strain HL-NP1T is proposed to represent a novel species of the genus

Jiella

, for which the name Jiella pelagia sp. nov. is proposed. The type strain is HL-NP1T (= KCCM 90499T = JCM 35838T).