bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unlocking the secrets of secrets: How can we learn about experiences that cannot be recreated in the laboratory?
Authors: Slepian Michael L. , Kalokerinos Elise K. 
Published: December 2023

AbstractPeople keep secrets for years with significant ramifications if the information were ever revealed. How can we understand the effects of long‐held secrets? The current paper presents a new perspective on secrecy and how it can be studied. By examining the multiple experiences people have with their multiple secrets, we can obtain a fuller view of how secrets affect people in daily life. Additionally, by examining a set of common secrets, across people, we can understand how secrets (i.e., exemplars) differ from one another, and we can study how those differences relate to important variables like well‐being. That is, rather than study a specific secret or secrecy situation (which will have limited generalizability), we can seek to study the entire universe of secrets, both to make generalizations across that universe and to compare different secrets to one another. Using the question of whether secrecy causes lower well‐being, we discuss this Multiple Exemplar Measurement approach alongside other methodologies. We highlight the many benefits of taking an exemplar‐level perspective, both for understanding secrecy and other psychological phenomena more broadly.
RIP‐Seq analysis of non‐PPR chloroplast editing factors reveals broad RNA interactions and enrichment of less efficiently translated RNAs by OZ1 and ORRM1 complexes
Authors: Hua Hope Y. , Santibanez Paola I. , Ngo Vinh T. , Hayes Michael L. 
Published: December 2023

SUMMARYC‐to‐U RNA editing in angiosperm chloroplasts requires a large suite of proteins bound together in the editosome. The editosome is comprised of PPR proteins, RIP/MORFs, OZ proteins, and ORRM proteins that physically interact in high molecular weight complexes. The specific functions of non‐PPR editing factors in the editosome are unclear, however, specific subsets of editing sites are affected by absence of non‐PPR editing factors. Unlike the PPR components of editosomes that have predictable nucleotide specificities, domains present in non‐PPR editing factors make RNA associations difficult to predict. In this study, chloroplast extracts were isolated from juvenile maize seedlings. RNAs were immunoprecipitated using polyclonal antibodies targeting non‐PPR editing factors RIP9, OZ1, and ORRM1. RNA libraries from duplicate experiments were compared. RIP9 was associated with most of the non‐ribosomal RNA content of chloroplasts, consistent with a general binding function to PPR L‐motifs and tethering of large ribonucleoprotein complexes. The breadth of RNA associations was greater than predicted and include mRNAs without predicted editing sites, tRNA sequences, and introns. OZ1 and ORRM1 were associated with a highly similar pool of RNAs that have a bias toward lower translational efficiency values in mature chloroplasts. Lower translational efficiency was also associated with the pool of edited RNAs compared to RNAs without editing sites. The unexpected breadth of interactions by non‐PPR editing factors suggests the editosome is large, diverse, and associated with RNAs with lower relative translational efficiency in mature chloroplasts.
Identification of two anti-
Candida
antibodies associated with the survival of patients with candidemia
Authors: Bromuro Carla , Posteraro Brunella , Murri Rita , Fantoni Massimo , Tumbarello Mario , Sanguinetti Maurizio , Dattilo Rosanna , Cauda Roberto , Cassone Antonio , Torosantucci Antonella 
Published: December 2023

ABSTRACT

We retrospectively studied antibody immunity in 92 candidemia patients, using sera taken at candidemia diagnosis. All patients showed the presence of IgG antibodies against all tested
Candida
antigens, namely Als3, Mp65, Hyr1 and Eno1, at levels significantly higher than those of non-candidemia controls. Both correlation and multivariable logistic regression analyses showed that the antibodies against Als3 and-Mp65, two known immunodominant and virulence-related proteins, were significantly associated with lower 30-day patient mortality. In particular, high titers of anti-Als3 antibodies were associated with survival in all subgroups of frail, more critical patients (over-median aged, infected by
C. albicans
or with septic shock) while high anti-Mp65 IgG levels were associated with survival in younger patients and in those infected by non-
albicans Candida
species or showing no signs of septic shock. A multivariable logistic model including anti-Als3 or anti-MP65 antibody levels and other variables, such as the serum β-glucan level at candidemia diagnosis, septic shock occurrence, the presence of diabetes, and initial antifungal treatment with fluconazole, was highly predictive of candidemia outcome, with an area under the curve of 0.85–0.86. Overall, the data demonstrate the ability of candidemia patients to mount a sustained memory antibody response to
Candida
antigens and that some of these responses have a sizeable impact on patient survival. Our data invite consideration of a multicenter, prospective investigation of antibody immunity in candidemia.

IMPORTANCE

Candidemia (bloodstream invasion by
Candida
species) is a major fungal disease in humans. Despite the recent progress in diagnosis and treatment, therapeutic options are limited and under threat of antimicrobial resistance. The disease mortality remains high (around 40%). In contrast with deep-seated invasive candidiasis, particularly that occurring in patients with hematologic malignancies and organ transplants, patients with candidemia are often not immunocompromised and therefore able to mount memory anticandidal immune responses, perhaps primed by
Candida
commensalism. We investigated antibody immunity in candidemia patients and report here on the ability of these patients to produce antibodies that react with
Candida
antigens. In particular, the patients with high titers of IgG reactive with two immunodominant, virulence-associated antigens (Als3 and MP65) had a higher 30-day survival. If confirmed by controlled, prospective clinical studies, our data could inform the development of antibody therapy to better treat a severe fungal infection such as candidiasis.
Campylobacter
prophage diversity reveals pervasive recombination between prophages from different
Campylobacter
species
Authors: Piña-González Adán Manuel , Castelán-Sánchez Hugo G. , Hurtado-Ramírez Juan Manuel , López-Leal Gamaliel 
Published: December 2023

ABSTRACT

Prophages, bacteriophages integrated into bacterial genomes, play a critical role in the genetic diversity and evolution of bacterial species. In this study, we investigated the prophage population harbored in
Campylobacter
species. A total of 446 high-quality and complete genomes of
Campylobacter
isolated from different sources revealed 431 prophages. We analyzed the phylogenomic relationships between 490 phages and prophages, unveiling a wide diversity of undescribed prophages. Bacteriophage pangenomes revealed shared genetic repertoires among different phage genera. In addition, we found recombination events between prophages from different phage genera, mainly in prophages infecting
Campylobacter jejuni
and
Campylobacter coli
, showing distinct evolutionary histories in specific regions of the prophage genomes. Specifically, these regions showed variations in gene content, enrichment in structural genes and others in hypothetical proteins, genes involved in transcription, DNA-associated factors, and genes associated with lysis. Finally,
Campylobacter
prophages alter the host genetic repertoire by carrying virulence factors and antibiotic-resistance genes.

IMPORTANCE

Prophages play an important role in shaping the genetic diversity and evolution of their hosts. Acquisition or loss of prophages can lead to genomic variations, including changes in the bacterial phenotype promoted by recombination events, genetic repertoire exchanges and dissemination of virulence factors, and antibiotic resistance. By studying prophages in
Campylobacter
species, scientists can gain insights into the evolutionary patterns, pathogenicity mechanisms, epidemiology, and population dynamics of these species. This has implications for public health, antibiotic resistance surveillance, and the development of targeted therapeutic approaches.
Lymphocyte and neutrophil count combined with intestinal bacteria abundance predict the severity of COVID-19
Authors: Chen Liuying , Yin Zhongwei , Zhou Dan , Li Xin , Yu Cheng , Luo Chang , Jin Yu , Zhang Lei , Song Jun , Rasche Leo , Einsele Hermann , Tu Lei , Zhou Xiang , Bai Tao , Hou Xiaohua 
Published: December 2023

ABSTRACT

Early identification of severe 2019 coronavirus disease (COVID-19) cases is of great significance. We included 92 COVID-19 patients and 22 healthy controls and collected their laboratory test data and stool for metagenomic sequencing analysis. We found that the proportion of severe COVID-19 cases was significantly increased in patients with reduced lymphocytes and elevated neutrophils and had unique intestinal microbiota.
Pseudothermotoga hypogea
and
Lachnospiraceae bacterium GAM79
were the species of bacteria that markedly decreased in COVID-19 patients compared to control individuals. For COVID-19 patients,
Enterococcus
sp.
DA9
,
Caldicellulosiruptor obsidiansis
, and
Enterococcus faecium
were the species of bacteria that significantly altered among patients with normal lymphocytes and neutrophils and patients with decreased lymphocytes and/or increased neutrophils, respectively. Fecal abundances of
Enterococcus
sp.
DA9
,
Prevotella intermedia
, and
Bifidobacterium dentium
were correlated with COVID-19 disease severity. Decreased lymphocytes and increased neutrophils, combined with decreased
Bifidobacterium dentium
and
Prevotella intermedia
, and increased
Enterococcus
sp.
DA9
have the highest power to predict severe cases of COVID-19 patients (area under receiver operating characteristic curve: 0.79). In conclusion, changes in the abundance of intestinal bacteria can reflect the severity of COVID-19 disease, and the combination with lymphocytes and neutrophils might be prognostic factors of COVID-19.

IMPORTANCE
The 2019 coronavirus disease (COVID-19) patients had a unique profile of gut bacteria. In this study, we characterized the intestinal bacteria in our COVID-19 cohorts and found that there was an increased incidence of severe cases in COVID-19 patients with decreased lymphocytes and increased neutrophils. Levels of lymphocytes and neutrophils and abundances of intestinal bacteria correlated with the severity of COVID-19.
Advances in the management of pancreatic cancer
Authors: Del Chiaro Marco , Sugawara Toshitaka , Karam Sana D , Messersmith Wells A 
Published: December 2023

Abstract
Pancreatic cancer remains among the malignancies with the worst outcomes. Survival has been improving, but at a slower rate than other cancers. Multimodal treatment, including chemotherapy, surgical resection, and radiotherapy, has been under investigation for many years. Because of the anatomical characteristics of the pancreas, more emphasis on treatment selection has been placed on local extension into major vessels. Recently, the development of more effective treatment regimens has opened up new treatment strategies, but urgent research questions have also become apparent. This review outlines the current management of pancreatic cancer, and the recent advances in its treatment. The review discusses future treatment pathways aimed at integrating novel findings of translational and clinical research.
Quality assessment of non-mydriatic fundus photographs for glaucoma screening in primary healthcare centres: a real-world study
Authors: Chen Qi , Zhou Mengtian , Cao Yang , Zheng Xuanli , Mao Huiyan , Lei Changrong , Lin Wanglong , Jiang Junhong , Chen Yize , Song Di , Xu Xiang , Ye Cong , Liang Yuanbo 
Published: December 2023

BackgroundThis study assessed the quality distribution of non-mydriatic fundus photographs (NMFPs) in real-world glaucoma screening and analysed its influencing factors.MethodsThis cross-sectional study was conducted in primary healthcare centres in the Yinzhou District, China, from 17 March to 3 December 2021. The quality distribution of bilateral NMFPs was assessed by the Digital Reading Department of the Eye Hospital of Wenzhou Medical University. Generalised estimating equations and logistic regression models identified factors affecting image quality.ResultsA total of 17 232 photographs of 8616 subjects were assessed. Of these, 11.9% of images were reliable for the right eyes, while only 4.6% were reliable for the left eyes; 93.6% of images were readable in the right eyes, while 90.3% were readable in the left eyes. In adjusted models, older age was associated with decreased odds of image readability (adjusted OR (aOR)=1.07, 95% CI 1.06~1.08, p<0.001). A larger absolute value of spherical equivalent significantly decreased the odds of image readability (all p<0.001). Media opacity and worse visual acuity had a significantly lower likelihood of achieving readable NMFPs (aOR=1.52, 95% CI 1.31~1.75; aOR=1.70, 95% CI 1.42~2.02, respectively, all p<0.001). Astigmatism axes within 31°~60° and 121°~150° had lower odds of image readability (aOR=1.35, 95% CI 1.11~1.63, p<0.01) than astigmatism axes within 180°±30°.ConclusionsThe image readability of NMFPs in large-scale glaucoma screening for individuals 50 years and older is comparable with relevant studies, but image reliability is unsatisfactory. Addressing the associated factors may be vital when implementing ophthalmological telemedicine in underserviced areas.Trial registration numberChiCTR2200059277.
Medication use of Canadians with chronic obstructive pulmonary disease: a cohort study
Authors: Stickland Michael K , Martins Karen J B , Sharpe Heather , Vu Ngoc Khanh , Bhutani Mohit , Walker Brandie L , Williamson Tyler , Bohlouli Solmaz , Richer Lawrence , Klarenbach Scott W 
Published: December 2023

ObjectivesThe objectives of this study were to describe medication use, treatment patterns and adherence, as well as acute exacerbations of chronic obstructive pulmonary disease (AECOPD) among adults living with COPD.MethodsA retrospective observational study using administrative data (linked by unique person-level personal health numbers) between 1 April 2007 and 31 March 2018 from Alberta, Canada was performed. Individuals aged ≥35 years who had been living with COPD ≥1 year on 1 April 2017 (index date) were identified. COPD-related medication use was determined on the index date (baseline), and medication use, treatment patterns, adherence and AECOPD were measured during the 1-year postindex observation period; descriptive statistics were applied.ResultsAmong the total cohort (n=192 814), 59% were not using a COPD-related medication at baseline; among those using medication, the most common (>10%) classes were short acting bronchodilators only (29%), dual inhaled corticosteroids/long acting beta2agonists (ICS/LABA, 27%), combined ICSs/LABA/long acting muscarinic antagonist (ICS/LABA/LAMA, 21%) and LAMA monotherapy (12%). During the observation period, those with baseline COPD medication use had low adherence (42% were adherent (medication possession ratio ≥0.80) to their baseline medication class) and AECOPD were common (13%–40%); 66% of those with ≥1 dispensation for an additional medication class had a step-up in therapy that was concordant with guideline recommendations.ConclusionsIn this population-based study, the majority of individuals identified as living with COPD were not taking any COPD-related medication, while in those who were taking medication, adherence was low, deficits in alignment to guideline-recommended therapy were observed and many had AECOPD. Strategies for earlier identification of undertreatment, consideration of guideline-based knowledge transfer strategies and mechanisms to improve long-term medication adherence may improve outcomes.
Theoretical investigation and optimization of rotation sensing in the new photonic crystal gyroscope based on the Sagnac effect using nonlinear photonic resonators
Authors: Mohammadi Masoud , Seifouri Mahmood , Olyaee Saeed 
Published: December 2023

In this research, the angular rotation speed in a passive photonic gyroscope based on the combination of side nanoring resonators and compensating waveguides has been analyzed by creating nonlinear effects in the control factors of the rings using the Sagnac effect. This structure consists of a central waveguide, two identical square resonators, and an almost U-shaped waveguide. The U-shaped waveguide causes coupling between the two resonators in a counterclockwise (CCW) mode. In this structure, a phase shift has been created in the output from the interference of two clockwise (CW) and CCW waves inside the resonators, and according to this phase shift and the central wavelength, the angular rotation speed has been estimated. In the proposed design of the gyroscope, by managing the nonlinear effects in the radius and refractive index (RI) of the coupling and inner rods, we have been able to control the changes in power, phase, and wavelength of the output from the device. With the increase in the intensity of power, the output power has an increasing slope at first, and at the point of creating a nonlinear effect in the sensor, the output power slope decreases. Also, this nonlinear effect directly affects the output phase of the structure. The maximum angular rotation speed in this gyroscope was [Formula: see text]/s. By changing the RI of the inner rods from 3.2 to 3.7, the maximum output-to-input power ratio changes from 0.38 W/[Formula: see text]m2 to 0.75 W/[Formula: see text]m2. By changing the radius of the coupling rods from 93 nm to 97 nm, the maximum power ratio decreases from 0.78 W/[Formula: see text]m2 to 0.55 W/[Formula: see text]m2. The field distribution profile and photonic bandgap in this gyroscope have been analyzed using the finite-difference time-domain (FDTD) and plane-wave expansion (PWE) methods, respectively. Also, the gyroscope has a footprint of 163.5 [Formula: see text]m2.
Mirror Mentoring: Black Women’s Experiences Serving as Mentors for Black Girls During a Virtual Computer Science Camp
Authors: Braswell Khalia , Smarr Simone , Payton Jamie 
Published: December 2023

Several studies have reported the positive benefits of informal Computer Science learning programs for Black girls, which include staff, mentors, and peers reflective of the girls in the program; however, we do not know enough about what motivates Black women to sign up to teach in such programs, or how representation in mentoring affects future CS learning for Black girls. Here we report the intersectional experiences of 11 Black women who served as instructors and mentors for the virtual INTech Summer Camp. The women in this study confirm that it is imperative to consider the intersectional experiences of Black women in CS as a whole, without explicating their identities. We found that Black women in CS feel that it is their responsibility to give back to Black girls to pay it forward from their own mentorship experiences. The Black women in our study describe seeking to fill a gap in mentorship that they experienced themselves, to share their knowledge and experiences to support the development of others who can relate to that intersection of identifying as Black and a girl or woman. Providing positive representation to encourage young Black girls to pursue tech careers is imperative to diversifying the tech workforce.
Symmetry Adapted Bases for Trigonometric Optimization
Authors: Metzlaff Tobias 
Published: December 2023

We present an algorithm to compute the global minimum of a trigonometric polynomial, when it is invariant under the exponential action of a Weyl group. This is based on a common relaxation technique that leads to a semi-definite program (SDP). It is then shown how to exploit the invariance in order to reduce the number of variables of the SDP and to simplify its structure significantly.
This approach complements the one that was proposed as a poster at the recent ISSAC 2022 conference [HMMR22] and later extended to [HMMR23]. In the previous work, we first used the invariance of the objective function to obtain a classical polynomial optimization problem on the orbit space and subsequently relaxed the problem to an SDP.
In the present work, we first apply the relaxation and then exploit symmetry. We show that the Weyl group action is induced by an orthogonal representation and describe its isotypic decomposition.
Efficacy and Safety of Trastuzumab Combined with Pertuzumab for Human Epidermal Growth Factor Receptor-2-Positive Breast Cancer: A Meta-Analysis Study of Randomized Control Trials
Authors: Gao Qingdong , Duan Xufang 
Published: December 2023

Objective. This systematic review was aimed to evaluate the efficacy and safety of trastuzumab in combination with pertuzumab for human epidermal growth factor receptor-2 (HER2)-positive breast cancer (BC). Methods. A comprehensive search of PubMed, Web of Science, Embase, China National Knowledge Internet, and Wanfang databases was conducted. All randomized controlled trials on trastuzumab in combination with pertuzumab for HER2-positive BC from the time of database construction to October 2022 were included. A meta-analysis of the included literature was performed using STATA 17.0 software. Results. A total of 8 studies were included, involving a total of 7628 patients, including 3814 patients in the treatment group and 3814 patients in the control groups. The results of the meta-analysis showed that the median progression-free survival was much shorter in the treatment group (trastuzumab combined with pertuzumab) than in the control group (placebo) (OR = 0.656, 95% CI (0.581, 0.741),

P

< 0.001) and that patients in the treatment group experienced significantly more cases of diarrhea than those in the control group (OR = 2.429, 95% CI (2.065, 2.856),

P

< 0.001) while experiencing significantly less cases of constipation (OR = 0.641, 95% CI (0.473, 0.869),

P

= 0.004). Notably, the incidence of nausea and vomiting did not differ significantly between the two groups. In addition, there was no significant difference between the two groups in the incidence of systemic adverse effects such as neutropenia, fatigue, myalgia, and cardiac disease (

P

> 0.05). However, the treatment group had a much higher incidence of rash than the control group (OR = 1.915, 95% CI (1.505, 2.437),

P

< 0.001). The risk of serious adverse reactions was markedly higher in patients in the treatment group than that in the control group (OR = 1.342, 95% CI (1.206, 1.494),

P

< 0.001). Conclusion. The combination of trastuzumab and pertuzumab was not effective in improving the intermediate progression-free survival of patients. However, adverse effects, including diarrhea and rash, are the limiting factors for the current promotion of this combination method.