bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Derivative-free Trust-region Method for Optimization on the Ellipsoid
Authors: Xie Pengcheng 
Published: October 2023

Abstract
Optimization methods play a crucial role in various fields and applications. In some optimization problems, the derivative information of the objective function is unavailable. Such black-box optimization problems need to be solved by derivative-free optimization methods. At the same time, optimization problems with ellipsoidal constraints are important and have widespread applications in various fields as well. Following the development of the late professor M. J. D. Powell’s efficient derivative-free trust-region optimization methods, this paper considers solving derivative-free optimization problems on the ellipsoid. Our new optimization solver EC-NEWUOA for problems on the ellipsoid in ℜ
n

is designed based on Powell’s derivative-free software NEWUOA for unconstrained optimization problems. The proposed techniques for our new method mainly include using the Courant penalty function, the augmented Lagrangian method, and the projection technique. Details about the method and theoretical analysis are included in this paper. We also compare our new method with other algorithms by solving test problems and then show the numerical advantages of our new method.
Ultra-quantum coherent states in a single finite quantum system
Authors: Vourdas A 
Published: October 2023

Abstract
A set of n coherent states is introduced in a quantum system with d-dimensional Hilbert space H(d). It is shown that they resolve the identity, and also have a discrete isotropy property. A finite cyclic group acts on the set of these coherent states, and partitions it into orbits. A n-tuple representation of arbitrary states in H(d), analogous to the Bargmann representation, is defined. There are two other important properties of these coherent states which make them ‘ultra-quantum’. The first property is related to the Grothendieck formalism which studies the ‘edge’ of the Hilbert space and quantum formalisms. Roughly speaking the Grothendieck theorem considers a ‘classical’ quadratic form

C

that uses complex numbers in the unit disc, and a ‘quantum’ quadratic form

Q

that uses vectors in the unit ball of the Hilbert space. It shows that if

C

⩽
1

, the corresponding

Q

might take values greater than 1, up to the complex Grothendieck constant

k

G

.

Q

related to these coherent states is shown to take values in the ‘Grothendieck region’

(
1
,

k

G

)

, which is classically forbidden in the sense that

C

does not take values in it. The second property complements this, showing that these coherent states violate logical Bell-like inequalities (which for a single quantum system are quantum versions of the Frechet probabilistic inequalities). In this sense also, our coherent states are deep into the quantum region.
Managing and monitoring a pandemic: showcasing a practical approach for the genomic surveillance of SARS-CoV-2
Authors: Jundzill Mateusz , Spott Riccardo , Lohde Mara , Hölzer Martin , Viehweger Adrian , Brandt Christian 
Published: October 2023

Abstract
With the rapidly growing amount of biological data, powerful but also flexible data management and visualization systems are of increasingly crucial importance. The COVID-19 pandemic has more than highlighted this need and the challenges scientists are facing. Here, we provide an example and a step-by-step template for non-IT personnel to easily implement an intuitive, interactive data management solution to manage and visualize the high influx of biological samples and associated metadata in a laboratory setting. Our approach is illustrated with the genomic surveillance for SARS-CoV-2 in Germany, covering over 11 600 internal and 130 000 external samples from multiple datasets. We compare three data management options used in laboratories: (i) simple, yet error-prone and inefficient spreadsheets, (ii) complex and long-to-implement laboratory information management systems and (iii) high-performance database management systems. We highlight the advantages and pitfalls of each option and outline why a document-oriented NoSQL option via MongoDB Atlas can be a suitable solution for many labs. Our example can be treated as a template and easily adapted to allow scientists to focus on their core work and not on complex data administration.
Insights into the Evolution of Ohnologous Sequences and Their Epigenetic Marks Post-WGD in Malus Domestica
Authors: Lallemand Tanguy , Leduc Martin , Desmazières Adèle , Aubourg Sébastien , Rizzon Carène , Landès Claudine , Celton Jean-Marc 
Published: October 2023

Abstract
A Whole Genome Duplication (WGD) event occurred several Ma in a Rosaceae ancestor, giving rise to the Maloideae subfamily which includes today many pome fruits such as pear (Pyrus communis) and apple (Malus domestica). This complete and well-conserved genome duplication makes the apple an organism of choice to study the early evolutionary events occurring to ohnologous chromosome fragments. In this study, we investigated gene sequence evolution and expression, transposable elements (TE) density, and DNA methylation level. Overall, we identified 16,779 ohnologous gene pairs in the apple genome, confirming the relatively recent WGD. We identified several imbalances in QTL localization among duplicated chromosomal fragments and characterized various biases in genome fractionation, gene transcription, TE densities, and DNA methylation. Our results suggest a particular chromosome dominance in this autopolyploid species, a phenomenon that displays similarities with subgenome dominance that has only been described so far in allopolyploids.
Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast
Authors: Sharp Nathaniel P , Smith Denise R , Driscoll Gregory , Sun Kexin , Vickerman Catherine M , Martin Sterling C T 
Published: October 2023

AbstractThe ribosomal DNA array in Saccharomyces cerevisiae consists of many tandem repeats whose copy number is believed to be functionally important but highly labile. Regulatory mechanisms have evolved to maintain copy number by directed mutation, but how spontaneous variation at this locus is generated and selected has not been well characterized. We applied a mutation accumulation approach to quantify the impacts of mutation and selection on this unique genomic feature across hundreds of mutant strains. We find that mutational variance for this trait is relatively high, and that unselected mutations elsewhere in the genome can disrupt copy number maintenance. In consequence, copy number generally declines gradually, consistent with a previously proposed model of rDNA maintenance where a downward mutational bias is normally compensated by mechanisms that increase copy number when it is low. This pattern holds across ploidy levels and strains in the standard lab environment but differs under some stressful conditions. We identify several alleles, gene categories, and genomic features that likely affect copy number, including aneuploidy for chromosome XII. Copy number change is associated with reduced growth in diploids, consistent with stabilizing selection. Levels of standing variation in copy number are well predicted by a balance between mutation and stabilizing selection, suggesting this trait is not subject to strong diversifying selection in the wild. The rate and spectrum of point mutations within the rDNA locus itself are distinct from the rest of the genome and predictive of polymorphism locations. Our findings help differentiate the roles of mutation and selection and indicate that spontaneous mutation patterns shape several aspects of ribosomal DNA evolution.
Structural Evolution of Gene Promoters Driven by Primate-Specific KRAB Zinc Finger Proteins
Authors: Farmiloe Grace , van Bree Elisabeth J , Robben Stijn F , Janssen Lara J M , Mol Lisa , Jacobs Frank M J 
Published: October 2023

Abstract
Krüppel-associated box (KRAB) zinc finger proteins (KZNFs) recognize and repress transposable elements (TEs); TEs are DNA elements that are capable of replicating themselves throughout our genomes with potentially harmful consequences. However, genes from this family of transcription factors have a much wider potential for genomic regulation. KZNFs have become integrated into gene-regulatory networks through the control of TEs that function as enhancers and gene promoters; some KZNFs also bind directly to gene promoters, suggesting an additional, more direct layer of KZNF co-option into gene-regulatory networks. Binding site analysis of ZNF519, ZNF441, and ZNF468 suggests the structural evolution of KZNFs to recognize TEs can result in coincidental binding to gene promoters independent of TE sequences. We show a higher rate of sequence turnover in gene promoter KZNF binding sites than neighboring regions, implying a selective pressure is being applied by the binding of a KZNF. Through CRISPR/Cas9 mediated genetic deletion of ZNF519, ZNF441, and ZNF468, we provide further evidence for genome-wide co-option of the KZNF-mediated gene-regulatory functions; KZNF knockout leads to changes in expression of KZNF-bound genes in neuronal lineages. Finally, we show that the opposite can be established upon KZNF overexpression, further strengthening the support for the role of KZNFs as bona-fide gene regulators. With no eminent role for ZNF519 in controlling its TE target, our study may provide a snapshot into the early stages of the completed co-option of a KZNF, showing the lasting, multilayered impact that retrovirus invasions and host response mechanisms can have upon the evolution of our genomes.
Vigor to Frailty As a Continuum—A New Approach in the Study of Muscle, Mobility, and Aging Cohort
Authors: Newman Anne B , Blackwell Terri L , Mau Theresa , Cawthon Peggy M , Coen Paul M , Cummings Steven R , Toledo Frederico G S , Goodpaster Bret H , Glynn Nancy W , Hepple Russell T , Kritchevsky Stephen B 
Published: October 2023

Abstract

Background
Frailty can occur in older adults without disability or multimorbidity. Current methods focus on the most frail, but poorly discriminate among those “not frail.”

Methods
The Study of Muscle, Mobility, and Aging (SOMMA) included 879 adults aged 70 years and older without mobility disability. We operationalized frailty domains using: peak oxygen consumption (endurance), digit symbol substitution test (speed), leg power (strength), perceived fatigability, D3 creatine dilution (sarcopenia), and accelerometry (sedentary behavior) to construct a frailty score of 0–12 summing tertiles (0–2) of each component. We used linear or logistic regression with and without adjustment for confounders to examine associations with age, reported, and performance function.

Results
The SOMMA frailty score distribution was broad and strongly associated with age (r = 0.33, p &lt; .0001). Each point was associated with a 30%–50% higher odds of having reported difficulty with activities of daily living or mobility. After grouping the total score (0–3, 4–7, and 8–12) those in the highest group were 9–31 times more likely to have functional limitation, and at least 8 times more likely to have poorer function after full adjustment. Higher scores identified those less likely to report ease of walking or higher physical activity. Peak oxygen consumption, leg power, fatigability, and digit symbol score contributed most to these associations.

Conclusions
The SOMMA frailty score characterizes frailty as a continuum from frail to vigorous with assessments that are amenable to change. Associations with age and function suggest utility for distinguishing a wide range of vigor and vulnerability in relatively well-functioning older adults.
Becoming Sandwiched in Later Life: Consequences for Individuals’ Well-Being and Variation Across Welfare Regimes
Authors: Albertini Marco , Lewin-Epstein Noah , Silverstein Merril , Tur-Sinai Aviad 
Published: October 2023

Abstract

Objectives
The experience of being sandwiched between support obligations towards both aging parents and adult offspring is likely to become more common and more relevant. We aim at assessing the effect of demographic and social sandwiching on the psychological health and subjective well-being of individuals experiencing these transitions, and to what extent, these effects vary across welfare regimes.

Methods
Data are from 63,585 individuals aged 50–75 participating in the Survey of Health, Ageing and Retirement in Europe (SHARE). We estimate within- and between-individual effects using hybrid regression models to predict depressive symptoms (EURO-D) and subjective well-being (control, autonomy, self-realization, and pleasure [CASP]).

Results
Among demographically sandwiched women, transitioning into social sandwiching and into supporting only parents was associated with a moderate but statistically significant increase in EURO-D and decline in CASP scores. The same association is not observed for male respondents. The pattern of variation among women living in countries characterized by different welfare regimes suggests that social sandwiching is less detrimental in Nordic regimes than in other welfare contexts.

Discussion
Results from the between-individuals part of the model indicate that there is a selection into social sandwiching of more healthy individuals into support roles. However, the within-individuals part of the model indicates that the transition into social sandwiching has a detrimental effect on women’s (but not men’s) psychological health and well-being. The explanations for this gendered effect of social sandwiching may be found in the “invisible” support provided by women and the gendered division of specific care tasks.
Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections
Authors: Aso Hirofumi , Ito Jumpei , Ozaki Haruka , Kashima Yukie , Suzuki Yutaka , Koyanagi Yoshio , Sato Kei 
Published: October 2023

Abstract

Background
Bats harbor various viruses without severe symptoms and act as their natural reservoirs. The tolerance of bats against viral infections is assumed to originate from the uniqueness of their immune system. However, how immune responses vary between primates and bats remains unclear. Here, we characterized differences in the immune responses by peripheral blood mononuclear cells to various pathogenic stimuli between primates (humans, chimpanzees, and macaques) and bats (Egyptian fruit bats) using single-cell RNA sequencing.

Results
We show that the induction patterns of key cytosolic DNA/RNA sensors and antiviral genes differed between primates and bats. A novel subset of monocytes induced by pathogenic stimuli specifically in bats was identified. Furthermore, bats robustly respond to DNA virus infection even though major DNA sensors are dampened in bats.

Conclusions
Overall, our data suggest that immune responses are substantially different between primates and bats, presumably underlying the difference in viral pathogenicity among the mammalian species tested.
The Distribution and the Antimicrobial Susceptibility Features of Microorganisms Isolated From the Burn Wounds: A 10-Year Retrospective Analysis
Authors: Özkaçmaz Ayşe , Dicle Yalçın , Bayram Yasemin , Parlak Mehmet , Akış Feride , Çallı İskan 
Published: October 2023

Abstract
In this study, we aimed to evaluate the distribution features and antimicrobial susceptibility test results of the microorganisms isolated from the wounds of pediatric and adult patients with burn. The culture and susceptibility test results of the microorganisms, isolated from the wound swabs of the patients hospitalized in a tertiary-burn care center in 10-year period, were retrospectively screened on the microbiology department databases. Their distribution of isolated microorganisms regarding species and susceptibility test results were compared with previous studies. A total of 367 microorganisms, isolated from the burn wounds of 293 patients (13 ± 18.9 years, F/M: 0.93) (73 adults and 220 pediatric patients), were included in this study. A solitary agent was isolated in 239 (81.6%) patients, while 2 were isolated in 43 (14.7%) and 3 or more agents in 11 (3.8%). From these, 33% of the isolated microorganisms were gram-positive cocci, 61% were gram-negative bacteria, and 6% were Candida spp. The most common isolated microorganisms were Staphylococcus aureus (18.5%), Pseudomonas spp. (16.9%), and Escherichia coli (11.2%), while the least common was Streptococcus spp. (2.5%). Methicillin resistance was 15% among the S. aureus strains. No resistance was observed against levofloxacin, vancomycin, teicoplanin, linezolid, daptomycin, fusidic acid, and tigecycline in S. aureus strains. The highest resistance rates were observed against levofloxacin (64%), tobramycin (64%), pip/tazobactam (63%), imipenem (63%), and the lowest against colistin (5%) and ceftazidime (29%), among Pseudomonas spp. The most common causative agents in burn wound infections and their current antimicrobial susceptibility features should be well identified, in order for prevention of serious complications and optimal management the condition to occur.
Alternation of the female form in Cambaridae (Decapoda: Astacidea) and the designation of a neotype for Procambarus clarkii (Girard, 1852) (Cambaridae: Decapoda)
Authors: Kawai Tadashi , McLay Colin L 
Published: October 2023

Abstract
The alternation of the female form is examined in eleven species of Cambaridae: Cambarus angularisHobbs & Bouchard, 1994, C. bartonii (Fabricius, 1798), Faxonius virilis (Hagen, 1870), Procambarus alleni (Faxon, 1884), P. clarkii (Girard, 1852), P. fallax (Hagen, 1870), P. pallidus (Hobbs, 1940), Cambarellus leslieiFitzpatrick & Laning, 1976, C. patzcuarensisVillalobos, 1943, C. schmittiHobbs, 1942, and C. shufeldtii (Faxon, 1884). All species show form-alternation in their annulus ventralis, that of Form I showing a cornified sinus and inflated fossa, but the Form-II females show a un-cornificed sinus and deflated fossa. Morphology of the Form-II annulus ventralis is similar to that of a juvenile. A wider abdomen in Form-I females occurred in five species (C. angularis, C. virilis, C. lesliei, C. schmitti, and C. shufeldtii), and inflation of the palm of the cheliped in Form-I females was observed in four (C. angularis, C. bartonii, F. virilis, and P. clarkii). The range of morphometric female-form alternation demonstrates four patterns: 1) wider abdomen and inflated chela (C. angularis, and C. bartonii), 2) wider abdomen and no chela inflation (C. lesliei, C. schmitti, and C. shufeldtii), 3) no wide abdomen and inflated chela (F. virilis and P. clarkii), 4) no wider abdomen and no chela inflation (P. alleni, P. pallidus, and P. fallax,). A neotype of P. clarkii is also designated and described.
Distal jejunal gallstone ileus—an unusual cause of bowel obstruction: a case report
Authors: Alamoodi Munaser 
Published: October 2023

Abstract
Gallstone ileus is a rare entity that causes bowel obstruction by gaining access through a cysto-enteric fistula. This is a case report of a 70-year-old man presenting with small bowel obstruction secondary to distal jejunal gallstone ileus impaction. He is not known to have any predisposing factors. He was managed effectively with an enterolithotomy. Early diagnosis is key to a good prognosis. Although other management options are available, enterolithotomy with or without cholecystectomy remains the gold standard of management.
The effect of emotional regulation difficulties on sexual and psychological distress using repetitive negative thinking as a mediator
Authors: Raposo Catarina F , Pascoal Patrícia M , Faustino Bruno , Nobre Pedro J 
Published: October 2023

Abstract

Background
Sexual distress, a determinant factor in diagnosing sexual dysfunction, plays a significant role in individuals’ sexual well-being, yet it has been overlooked in research.

Aim
This exploratory study adopted a transdiagnostic approach to sexual distress and sought to examine the association between emotional regulation difficulties and sexual and psychological distress, with repetitive negative thinking as a potential mediator.

Methods
We used a quantitative cross-sectional design with a sample of 509 partnered individuals.

Outcomes
The survey included a sociodemographic questionnaire, the Difficulties in Emotion Regulation Scale–Short Form, the Kessler Psychological Distress Scale, the Persistent and Intrusive Negative Thoughts Scale, and the Female Sexual Distress Scale–Revised.

Results
Correlational analysis revealed significant associations among emotional regulation difficulties, repetitive negative thinking, psychological distress, and sexual distress. Furthermore, a mediation model demonstrated that repetitive negative thinking significantly mediated emotion dysregulation and psychological and sexual distress.

Clinical Implications
These findings underscore the importance of considering emotion regulation difficulties and repetitive negative thinking as a maladaptive coping strategy when evaluating sexual distress and suggest that therapeutic interventions targeting such difficulties and thoughts may yield beneficial outcomes.

Strengths and Limitations
These findings reinforce the importance of considering the role of emotional regulation difficulties and, consequently, repetitive negative thinking as a dysfunctional coping strategy, when studying and intervening in sexual distress. Future research with clinical samples should be developed to establish better the significance of considering these two dimensions in assessment and therapeutic intervention.

Conclusion
Future research should corroborate and expand upon these findings to advance our understanding of sexual distress and optimize interventions in this domain.