bluuebunny/crossref_metadata_2025 huggingface dataset:
ADViSELipidomics: a workflow for analyzing lipidomics data
Authors: Del Prete Eugenio , Campos Ana Margarida , Della Rocca Fabio , Gallo Carmela , Fontana Angelo , Nuzzo Genoveffa , Angelini Claudia
Published: October 2022

ADViSELipidomics is a novel Shiny app for preprocessing, analyzing and visualizing lipidomics data. It handles the outputs from LipidSearch and LIQUID for lipid identification and quantification and the data from the Metabolomics Workbench. ADViSELipidomics extracts information by parsing lipid species (using LIPID MAPS classification) and, together with information available on the samples, performs several exploratory and statistical analyses. When the experiment includes internal lipid standards, ADViSELipidomics can normalize the data matrix, providing normalized concentration values per lipids and samples. Moreover, it identifies differentially abundant lipids in simple and complex experimental designs, dealing with batch effect correction. Finally, ADViSELipidomics has a user-friendly graphical user interface and supports an extensive series of interactive graphics.

Availability and implementation

ADViSELipidomics is freely available at https://github.com/ShinyFabio/ADViSELipidomics

Supplementary information

Supplementary data are available at Bioinformatics online.
A method for multiple sampling mouse sperm in vivo
Authors: Moreno-del Val Gonzalo , Muñoz-Robledano Patricia , Caler Antonio J , Morante Javier
Published: October 2022

Mice are the most widely used animal model to study human diseases. However, the difficulty of in vivo recovery of mouse sperm has posed a limitation with its use in reproductive biology research. Several published techniques for obtaining sperm samples in vivo have been described, but most of them have several caveats. Critical limitations include poor reliability and significant mortality (Electroejaculation and drug-induced ejaculation), or the need for a large number of animals, careful programming, and laborious work (directed mating). Here, we describe a new approach for in vivo collection of sperm in the mouse via direct puncture of the epididymis to address these limitations. In addition, the technique is easy, safe, and reliable, allowing the animal to recover and maintain its fertility. In this way, punctual experiments could be carried out, or even more so, serial sampling of the same animal over time. Therefore, our approach allows for long-term and time-course experiments to study sperm characteristics under different treatments or conditions while maintaining the spermatogenic niche in vivo. In summary, we present our original approach as a powerful research tool to facilitate the study of spermatozoa relevant to various areas of biomedical research.
Visualization of preimplantation uterine fluid absorption in mice using Alexa Fluor™ 488 Hydrazide
Authors: Li Yuehuan , Martin Taylor Elijah , Hancock Jonathan Matthew , Li Rong , Viswanathan Suvitha , Lydon John P , Zheng Yi , Ye Xiaoqin
Published: October 2022

Uterine fluid plays important roles in supporting early pregnancy events and its timely absorption is critical for embryo implantation. In mice, its volume is maximum on day 0.5 post-coitum (D0.5) and approaches minimum upon embryo attachment ~D4.0. Its secretion and absorption in ovariectomized rodents were shown to be promoted by estrogen and progesterone (P4), respectively. The temporal mechanisms in preimplantation uterine fluid absorption remain to be elucidated. We have established an approach using intraluminally injected Alexa Fluor™ 488 Hydrazide (AH) in preimplantation control (RhoAf/f) and P4-deficient RhoAf/fPgrCre/+ mice. In control mice, bulk entry (seen as smeared cellular staining) via uterine luminal epithelium (LE) decreases from D0.5 to D3.5. In P4-deficient RhoAf/fPgrCre/+ mice, bulk entry on D0.5 and D3.5 is impaired. Exogenous P4 treatment on D1.5 and D2.5 increases bulk entry in D3.5 P4-deficient RhoAf/fPgrCre/+ LE, while progesterone receptor (PR) antagonist RU486 treatment on D1.5 and D2.5 diminishes bulk entry in D3.5 control LE. The abundance of autofluorescent apical fine dots, presumptively endocytic vesicles to reflect endocytosis, in the LE cells is generally increased from D0.5 to D3.5 but its regulation by exogenous P4 or RU486 is not obvious under our experimental setting. In the glandular epithelium (GE), bulk entry is rarely observed and green cellular dots do not show any consistent differences among all the investigated conditions. This study demonstrates the dominant role of LE but not GE, the temporal mechanisms of bulk entry and endocytosis in the LE, and the inhibitory effects of P4-deficiency and RU486 on bulk entry in the LE in preimplantation uterine fluid absorption.
Utility of Circulating Free DNA Fragmentomics in the Prediction of Pathological Response after Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer
Authors: Wang Yaqi , Fan Xiaojun , Bao Hua , Xia Fan , Wan Juefeng , Shen Lijun , Wang Yan , Zhang Hui , Wei Yulin , Wu Xue , Shao Yang , Li Xinxiang , Xu Ye , Cai Sanjun , Zhang Zhen
Published: October 2022

Background

A "Watch and Wait” (W&W) approach has become an alternative to surgery for locally advanced rectal cancer (LARC) after neoadjuvant chemoradiotherapy (nCRT). Precise prediction of pathological complete response (pCR) will improve patient selection for W&W. We investigated the utility of cell-free DNA (cfDNA) fragmentomics in predicting pCR.

Methods

We recruited 119 LARC patients and evaluated nCRT response by pCR status and pathological or MRI tumor regression grade (mrTRG). Plasma samples before, during, and after nCRT were applied to deep targeted-panel sequencing, with 103 patients having complete samples. cfDNA fragment and 5′-end motif profiles were used to construct elastic-net logistic regression models to predict non-pCR. Predictive performance was measured by area under the receiver operator characteristic curve (AUC), sensitivity, and specificity.

Results

In the training cohort, the model based on 5′-end motif profile plus mrTRG achieved the highest cross-validation AUC (0.92, 95% CI, 0.91–0.93). The AUC in a testing cohort was 0.96 (95% CI, 0.90–1.00). The models based on 5′-end motif profile alone or in combination with mrTRG both maintained good predictive ability for patients without detectable circulating tumor DNA (AUC 0.94, 95% CI, 0.93–0.95; AUC 0.95, 95% CI, 0.94–0.96). In an external validation cohort, the model trained with a local 5′-end motif profile obtained an AUC of 0.878 (95% CI, 0.801–0.956) in discriminating colorectal cancer from healthy subjects.

Conclusions

The combination of a 5′-end motif profile with mrTRG has the potential to predict the response to nCRT, and therefore may improve the patient selection for a W&W approach.
The Need for Being Explicit: Failed Attempts to Construct Implicit Certificates from Lattices
Authors: Bindel Nina , McCarthy Sarah
Published: October 2022

Global efforts such as the National Institute of Standards and Technology (NIST)’s post-quantum standardization center on cryptographic primitives like public-key encryption and signature schemes that are secure even in the presence of quantum adversaries. In addition, one must also consider efficient certificate management as new technologies like the Internet of Things and 5G wireless networks rely on them. For example, the IEEE Standard for vehicle-to-vehicle communication depends on implicit certificates. However, the only efficient construction available is over elliptic curves, and hence not quantum-secure. This paper investigates approaches to construct implicit certificate schemes from lattices, employing the NIST Round 3 signature schemes Dilithium and Falcon. We consider emulation of the existing implicit certificate scheme and proceed to more innovative techniques like combining the two schemes or pairing them with encryption. Unfortunately, we encounter problems with each design, due to recurring causes like conflicting secret key and signature sizes, unique sampler requirements and the rigidity of the parameter sets. By explaining each of these issues, this paper will hopefully spark ideas for more successful constructions.
Rainbow Tables: How Far Can CPU Go?
Authors: Avoine Gildas , Carpent Xavier , Leblanc-Albarel Diane
Published: October 2022

Rainbow tables are techniques commonly used in computer security to invert one-way functions, for instance to crack passwords, when the domain of definition is reasonably sized. This article explores the limit on the problem size that can be treated by rainbow tables when the precomputation and the attack phases are both CPU-driven. We conclude that the bottleneck is no longer the memory as it may have been and the precomputation phase seems to have been underestimated so far. We offer a comparison of what can be done on different environments depending on the needs and available computing power of the users.
Impacts of anterior-posterior jaw disproportions on speech of dentofacial disharmony patients
Authors: Oliver Steven , Keyser Mary Morgan Bitler , Jhingree Samantha , Bocklage Clare , Lathrop Hillary , Giduz Natalie , Moss Kevin , Blakey George , White Raymond , Turvey Timothy , Mielke Jeff , Zajac David , Jacox Laura Anne
Published: October 2022

Background/Objectives

Articulation problems impact communication, development, and quality of life, and are diagnosed in 73–87% of patients with Class II Dentofacial Disharmony (DFD). We evaluated whether differences exist in stop (/t/ or/k/), fricative (/s/ or/ʃ/), and affricate (/tʃ/) consonant sounds of Class II DFD subjects, and whether extent of malocclusion correlates with severity of speech distortion. We hypothesized that Class II patients display milder distortions than Class III and anterior open bite (AOB), as Class II patients can posture into a Class I occlusion.

Materials/Methods

Audio and orthodontic records were collected from DFD patients (N = 53-Class II, 102-Class III, 72-Controls) who were pursuing orthodontics and orthognathic surgery. A speech pathologist perceptually scored speech. Acoustic differences in recordings were measured using Spectral Moment Analysis.

Results

When Class II subjects were compared to controls, significant differences were found for the centroid frequency (M1) of the /s/ sound and the spectral spread (M2) of /t/, /tʃ/, and /s/ sounds, with pairwise significance for controls relative to Class II AOB and all Class II subjects. Class II AOB subjects had higher M1 and M2 values than patients with Class II closed bites and Class I controls for most sounds. When comparing across anterior-posterior (AP) groups, differences exist between controls, Class II and III DFD subjects for M1 of /t/, /tʃ/, and/ʃ/ and M2 for /t/, /tʃ/, /s/, and /ʃ/ sounds. Using linear regression, correlations between Class II and III severity and spectral measures were found for /t/ and /tʃ/ sounds.

Conclusions/Implications

Class II and III patients have a higher prevalence of qualitative distortions and spectral changes in consonants compared to controls, but Class II spectral shifts are smaller and affect fewer sounds than in Class III and AOB cohorts. Linear correlations between AP discrepancy and spectral change suggest causation and that treatment may improve articulation problems.
Decolonizing business English: exploring classroom ideologies
Authors: Banister Chris
Published: October 2022

The inherent coloniality of ELT, as both driver and product of Anglophone political power, poses particular challenges for ELT teachers and learners looking to engage with decolonizing agendas. With only scant evidence of these agendas translating into ELT practice, I explored decolonial options, counter-hegemonic actions, with my undergraduate business English learners, adopting a form of practitioner research known as exploratory practice, and centring enquiry on our use of business news articles for a key course component. My learners revealed the potential of decolonial options, and the reflective, exploratory process exposed our language ideologies, with a vocal minority of students resisting any end to the established English-only policy. Suggestions are offered for fellow ELT teachers working in similar settings and who are interested in exploring their own use of authentic materials through a decolonizing lens.
Challenges and Opportunities for Advancing Research and Improving Care for Sexual and Gender Minorities With Inflammatory Bowel Disease
Authors: Boyd Taylor , Friedman Sonia
Published: October 2022

Lay Summary

Within the field of gastroenterology and inflammatory bowel disease specifically, there has been little research exploring the healthcare experiences of LGBTQIA+ individuals. This article describes unique clinical challenges and research opportunities that exist particularly at the intersection of inflammatory bowel disease and sexual health.
Expanding the history of humanities computing: Hugh Kenner’s conversational criticism
Authors: Roach Rebecca
Published: October 2022

This article posits that a novel and humanistic model of computing—‘conversational computing’—would emerge in the 1960s which, despite being largely forgotten today, proved extremely influential in computing and wider culture. I examine the metaphor and model of conversation embedded in this earlier idea and trace the ways it was taken up in the humanities via examining, through his archives, the career of renowned literary critic and programmer, Hugh Kenner (1923–2003).
Illusions of objectivity: The two functions of country of origin information in asylum assessment
Authors: Bodström Erna
Published: October 2022

The article argues that the intertextuality of country of origin information (COI) plays a significant part in constructing asylum decisions and therefore the lives and futures of those affected by forced migration. COI in asylum decisions is based on COI reports, which in turn are based on other COI reports, interviews, or media materials. This makes them intertextual, that is, referring to and transforming other texts. That is, COI reports typically include dozens or even hundreds of pages of information, which are abbreviated in order to be used in a few paragraphs of asylum decisions. This is done through recontextualisation, that is, by selecting certain parts of the text and reformulating them to the new context. The article analyses COI in 67 negative first-instance asylum decisions and in 38 COI reports and similar sources through the concept of intertextuality. It argues that COI has two functions in the asylum decisions, personal and general. Personal COI is used to assess the truthfulness of the asylum applicant’s persecution narrative, whereas general COI is used to evaluate the overall security and human rights situation in the country of origin. The article shows that even though the decisions tend to present COI as objective information, it can easily be biased, irrelevant, and illogical, therefore creating an illusion of objectivity.
Head Face and Neck Surgeon Deployment in the New French Role 2: The Damage Control Resuscitation and Surgical Team
Authors: Fawaz Rayan , Dagain Arnaud , Pons Yoann , Haen Pierre , Froussart Françoise , Caruhel Jean Baptiste
Published: October 2022

Introduction

High-intensity conflict is back after decades of asymmetric warfare. With the increase in the incidence of head, face, and neck (HFN) injuries, the French Medical Military Service has decided to deploy HFN surgeons in the new French Role 2: the Damage Control, Resuscitation, and Surgical Team (DCRST). This study aims to provide an overview of HFN French surgeons from their initial training, including the surgical skills required, to their deployment on the DCRST.

Materials and Methods

The DCRST is a tactical mobile medico-surgical structure with several configurations depending on the battlefield, mission, and flux of casualties. It represents the new French paradigm for the management of combat casualties, including HFN injuries.

Results

The HFN’s military surgeon training starts during residency with rotation in the different subspecialties. The HFN surgeon follows a training course called “The French Course for Deployment Surgery” that provides sufficient background to manage polytrauma, including HFN facilities on modern warfare. We have reviewed the main surgical procedures required for an HFN military surgeon.

Conclusion

The systematic deployment of HFN surgeons in Role 2 is a specificity of the French army as well as the HFN surgeon’s training.

Currently, the feedback from an asymmetric conflict is encouraging. However, it will have to innovate to adapt to modern warfare.
Origin and chromatin remodeling of young X/Y sex chromosomes in catfish with sexual plasticity
Authors: Gong Gaorui , Xiong Yang , Xiao Shijun , Li Xi-Yin , Huang Peipei , Liao Qian , Han Qingqing , Lin Qiaohong , Dan Cheng , Zhou Li , Ren Fan , Zhou Qi , Gui Jian-Fang , Mei Jie
Published: October 2022

Assembly of a complete Y chromosome is a significant challenge in animals with an XX/XY sex-determination system. Recently, we created YY-supermale yellow catfish by crossing XY males with sex-reversed XY females, providing a valuable model for Y-chromosome assembly and evolution. Here, we assembled highly homomorphic Y and X chromosomes by sequencing genomes of the YY supermale and XX female in yellow catfish, revealing their nucleotide divergences with only less than 1% and with the same gene compositions. The sex-determining region (SDR) was identified to locate within a physical distance of 0.3 Mb by FST scanning. Strikingly, the incipient sex chromosomes were revealed to originate via autosome–autosome fusion and were characterized by a highly rearranged region with an SDR downstream of the fusion site. We found that the Y chromosome was at a very early stage of differentiation, as no clear evidence of evolutionary strata and classical structure features of recombination suppression for a rather late stage of Y-chromosome evolution were observed. Significantly, a number of sex-antagonistic mutations and the accumulation of repetitive elements were discovered in the SDR, which might be the main driver of the initial establishment of recombination suppression between young X and Y chromosomes. Moreover, distinct three-dimensional chromatin organizations of the Y and X chromosomes were identified in the YY supermales and XX females, as the X chromosome exhibited denser chromatin structure than the Y chromosome, while they respectively have significantly spatial interactions with female- and male-related genes compared with other autosomes. The chromatin configuration of the sex chromosomes as well as the nucleus spatial organization of the XX neomale were remodeled after sex reversal and similar to those in YY supermales, and a male-specific loop containing the SDR was found in the open chromatin region. Our results elucidate the origin of young sex chromosomes and the chromatin remodeling configuration in the catfish sexual plasticity.
Enthymising
Authors: Del Mar Maksymilian
Published: October 2022

This article offers, through a reading of James Fredal’s new study, The Enthymeme, an argument for the value of the history of rhetoric to theories of legal reasoning. The argument is inspired by Fredal’s call, in his ingenious reading of the practice of Ancient Greek oratory, for a shift in thinking of the enthymeme as a logical form, and an inadequate or imperfect one (when compared to the logical forms of dialectic), towards a way of thinking that emphasises enthymising as an activity, and specifically a relational and interactive activity of making narrative. At the heart of legal reasoning, on this view, is narrativity, which has two related elements: (i) the arts of storytelling and (ii) the arts of storyworld construction, or actively and creatively experiencing the told. What makes a narrative difference—for instance, various kinds of enthymising, or bringing to mind of narrative details—also makes a normative one. Enthymising, understood in this way, thus offers a way of understanding legal reasoning as a rhetorical art of making narratives that is deeply emotional, embodied and sensory. This art illuminates not only the making of arguments by advocates in particular cases, but also the making of law by judges and others over time.
Quantification of Needle Angles for Traditional Lumbar Medial Branch Radiofrequency Ablation: An Osteological Study
Authors: Tran John , Campisi Emma S , Agur Anne M R , Loh Eldon
Published: October 2022

Background

Clinical outcomes following lumbar medial branch radiofrequency ablation (RFA) have been inconsistent. One possible reason is less-than-optimal placement of the electrode along the medial branch at the lateral neck of superior articular process (SAP). Needle angles that define optimal placement (i.e., parallel to the medial branch) may be helpful for consistent technical performance of RFA. Despite its importance, there is a lack of anatomical studies that quantify RFA needle placement angles.

Objective

To quantify and compare needle angles to achieve parallel placement along the medial branch as it courses on the middle two-quarters of the lateral neck of the SAP at the L1–L5 vertebrae.

Design

Osteological Study.

Methods

Ten lumbar vertebral columns were used in this study. Needles were placed along the periosteum of the middle two-quarters of the lateral neck of SAP. Mean needle angles for L1–L5 were quantified and compared using posterior (n = 100) and lateral (n = 100) photographs.

Results

Mean needle angles varied ranging from 29.29 ± 17.82° to 47.22 ± 16.27° lateral to the parasagittal plane (posterior view) and 33.53 ± 10.23° to 49.19 ± 10.69° caudal to the superior vertebral endplate (lateral view). Significant differences in mean angles were found between: L1/L3 (P = .008), L1/L4 (P = .003), and L1/L5 (P = .040) in the posterior view and L1/L3 (P = .042), L1/L4 (P < .001), L1/L5 (P < .001), L2/L4 (P = .004), and L2/L5 (P = .004) in lateral view.

Conclusions

Variability of needle angles suggest a standard “one-size-fits-all” approach may not be the optimal technique. Future research is necessary to determine optimal patient-specific needle angles from a more detailed and granular analysis of fluoroscopic landmarks.
Effects of bond-randomness and Dzyaloshinskii–Moriya interactions on the specific heat at low temperatures of a spherical kagomé cluster in {W72V30}
Authors: Motohashi Mikio , Inoue Kouki , Morita Katsuhiro , Fukumoto Yoshiyuki , Nakano Hiroki
Published: October 2022

For the spin-1/2 spherical kagomé cluster, as well as for the 2D kagomé lattice, many low-energy singlet excitations have been expected to exist in the energy region below the spin gap, which has been actually confirmed by Kihara et al. in their specific heat measurements up to 10 K in {W72V30}, for which the exchange interaction was estimated as J = 115 K. However, the experimental result of the specific heat cannot be reproduced by the theoretical result in the Heisenberg model. Although the theoretical result has a peak around 2 K, the experimental one does not. To elucidate this difference, we incorporate Dzyaloshinskii–Moriya (DM) interactions and bond-randomness into the model Hamiltonian for {W72V30} and calculate the density of states, entropy, and specific heat at low temperatures by using the Lanczos method. We find that DM interactions do not significantly affect the energy distribution of about 10 singlet states above the ground state, which are involved in the peak structure of the specific heat around 2 K, while even 10% bond-randomness disperses this distribution to collapse the 2 K peak. Kihara et al. also reported experimental specific heats under magnetic fields up to 15 T (= 0.17J), and found that the specific heats show almost no magnetic field dependence, which strongly suggests that the bond-randomness is much stronger than the magnetic fields. For example, our calculated specific heats with 50% randomness reproduce the experimental ones up to about 5 K.
Real-world effectiveness and safety of tofacitinib and abatacept in patients with rheumatoid arthritis
Authors: Hirose Wataru , Harigai Masayoshi , Amano Koichi , Hidaka Toshihiko , Itoh Kenji , Aoki Kazutoshi , Nakashima Masahiro , Nagasawa Hayato , Komano Yukiko , Nanki Toshihiro
Published: October 2022

Objective

We compared the 52-week effectiveness and safety of tofacitinib (TOF) and abatacept (ABT) in patients with RA in a real-world setting and investigated a role of human leucocyte antigens (HLA)-DRB1 shared epitope (SE) in the effectiveness.

Methods

RA patients starting TOF (n = 187) and ABT (n = 183) were enrolled. Effectiveness was compared after reducing the selection bias to a minimum using the inverse probability of treatment weighting (IPTW) based on propensity scores. The influence of SE alleles on effectiveness was compared within each treatment group. A treatment group comparison was also performed within SE-positive and SE-negative groups.

Results

Herpes zoster and some laboratory abnormalities were more frequent in the TOF group than in the ABT group. Patient characteristics did not differ significantly between treatment groups after adjustments with IPTW. The TOF group had a significantly higher proportion of DAS in 28 joints using ESR (DAS28-ESR) remission at week 52 than the ABT group. The DAS28-ESR at week 12 and thereafter was not affected by the copy number of SE alleles in the TOF group, but decreased significantly as the copy number increased in the ABT group. In SE-positive patients, remission and drug retention rates did not differ significantly between the two treatment groups. In SE-negative patients, the TOF group showed significantly higher remission and drug retention rates than the ABT group.

Conclusion

The present results suggest that TOF is more effective with regard to remission at week 52 based on treatment responses in SE-negative RA patients.
Injectable and biofunctionalized fibrin hydrogels co-embedded with stem cells induce hair follicle genesis
Authors: Chen Haiyan , Ma Xiaoxiao , Zhang Mengqi , Liu Zhonghua
Published: October 2022

Fibrin-based hydrogels have been widely used in various tissue engineering because of their biocompatibility, biodegradability, tunable mechanical characteristics and nanofibrous structural properties. However, their ability to support stem cells for hair follicle neogenesis is unclear. In this study, we investigated the effect of fibrin hydrogels in supporting skin-derived precursors (SKPs) in hair follicle neogenesis. Our results showed that SKPs in fibrin hydrogels with high cell viability and proliferation, the stemness of SKPs could be maintained, and the expression of hair induction signature genes such as akp2 and nestin was enhanced. Moreover, hair follicle reconstruction experiments showed de novo hair genesis in mice and the hairs persisted for a long time without teratoma formation. More importantly, the blood vessels and sebaceous glands were also regenerated. Our study demonstrated that fibrin hydrogels are promising in hair follicle regeneration and have potential application in clinical settings for alopecia and wound healing.
Peer review in funding-by-lottery: A systematic overview and expansion
Authors: Shaw Jamie
Published: October 2022

Despite the surging interest in introducing lottery mechanisms into decision-making procedures for science funding bodies, the discourse on funding-by-lottery remains underdeveloped and, at times, misleading. Funding-by-lottery is sometimes presented as if it were a single mechanism when, in reality, there are many funding-by-lottery mechanisms with important distinguishing features. Moreover, funding-by-lottery is sometimes portrayed as an alternative to traditional methods of peer review when peer review is still used within funding-by-lottery approaches. This obscures a proper analysis of the (hypothetical and actual) variants of funding-by-lottery and important differences amongst them. The goal of this article is to provide a preliminary taxonomy of funding-by-lottery variants and evaluate how the existing evidence on peer review might lend differentiated support for variants of funding-by-lottery. Moreover, I point to gaps in the literature on peer review that must be addressed in future research. I conclude by building off of the work of Avin in moving toward a more holistic evaluation of funding-by-lottery. Specifically, I consider implications funding-by-lottery variants may have regarding trust and social responsibility.
Using the Health Belief Model to Examine Adherence to Preventive Measures Among Nursing Students During COVID-19
Authors: Okoli Chizimuzo , Brouwer Kent R. , Walmsley Lee Anne
Published: October 2022

Associations between health belief model constructs and engagement in COVID-19 preventive practices were examined in a population of 234 nursing students. Most (93 percent/68 percent, respectively) reported occasionally/frequently performing 6-feet physical distancing and wearing face masks/covering in public. Among health belief model constructs, perceived benefits were significantly associated with practicing physical distancing; perceived barriers were associated with lower likelihood. Perceived self-efficacy was associated with a greater likelihood of wearing face masks/covering in public. Nursing students should be provided timely and relevant information on preventive measures based on the recognition of different risk appraisals among students.
Student Perspectives on Sources of Resilience During Nursing School
Authors: Mayer Kala A. , MacMillan Natalie K. , Linehan Kate J.
Published: October 2022

Resilience is important to the academic and career success of nursing students; however, the literature on nursing student resilience is sparse and remains undertheorized. This article describes nursing students’ perspectives on sources of resilience during nursing school at one institution of higher learning. A constant comparative analysis of baccalaureate nursing student focus group responses was performed. Three themes emerged: negative experiences, supportive structures and relationships, and individual coping processes and abilities. Interrelationships between thematic findings highlight the centrality of supportive structures and relationships. Based on these findings, theoretical guidance for future nursing student resilience assessments and interventions is provided.
Increasing Critical Thinking Opportunities Through Post-Conference Simulation in a Pediatric Baccalaureate Nursing Course
Authors: Andries Chelsey , Hall Katie , McCullough Amanda
Published: October 2022

Traditional clinical experiences offer opportunities for nursing students to practice critical thinking. However, there are many limitations to planning these clinical experiences. The purpose of this educational activity is to incorporate post-conference simulation with traditional clinical to allow undergraduate nursing students expanded opportunities for enhancing critical thinking. The faculty created high-acuity simulation scenarios, which included a child experiencing respiratory, hematologic, neurological, or cardiovascular complications. After participating in the activity, students completed evaluation and reported increased confidence and preparedness to identify, think critically, and intervene in high-acuity situations.
Association of Occupational Stress With Tinnitus Among Career Firefighters in the United States
Authors: Odes Rachel , Chin Dal Lae , Li Jian , Hong OiSaeng
Published: October 2022

Objective

This study explores the relationship between occupational stress and tinnitus among firefighters, a group often exposed to two tinnitus risk factors: high stress and noise.

Methods

This cross-sectional study includes 240 firefighters in the United States. Data describing demographic characteristics, occupational stress, noise exposure, and tinnitus were collected by survey. Occupational stress was measured using the short version of the Effort-Reward Imbalance Questionnaire.

Results

Forty-three percent of participants reported experiencing tinnitus within the past month. For occupational stress, higher effort (odds ratio, 1.25; 95% confidence interval, 1.05 to 1.49) and higher effort-reward ratio (odds ratio, 12.28; 95% confidence interval, 3.08 to 48.86) were associated with increased odds of tinnitus, after adjustment for demographic characteristics and noise exposure.

Conclusions

Occupational stress may increase the likelihood of tinnitus for firefighters, an already at-risk group of workers. Health providers should incorporate stress assessment into tinnitus management programs.
Data Set for Reporting of Uterine Malignant and Potentially Malignant Mesenchymal Tumors: Recommendations From the International Collaboration on Cancer Reporting (ICCR)
Authors: Nucci Marisa R. , Webster Fleur , Croce Sabrina , George Suzanne , Howitt Brooke E. , Ip Philip P.C. , Lee Cheng-Han , Rabban Joseph T. , Soslow Robert A. , van der Griend Rachael , Lax Sigurd F. , McCluggage W. Glenn
Published: October 2022

The International Collaboration on Cancer Reporting (ICCR) seeks to produce standardized, evidence-based protocols for the reporting of tumors with the aim of ensuring that all cancer reports generated worldwide will be of similar high quality and record the same elements. Herein, we describe the development of the data set for the reporting of uterine malignant and potentially malignant mesenchymal tumors by a panel of expert pathologists and a single clinician and provide the commentary and rationale for the inclusion of core and noncore elements. This data set, which incorporates the recent updates from the 5th edition of the World Health Organization Classification of Female Genital Tumors, addresses several subjects of debate including which mesenchymal tumors should be graded, how to document extent of invasion, mitotic counts, and the role of ancillary testing in tumor diagnosis and patient management. The inclusion of elements is evidence-based or based on consensus of the expert panel with clinical relevance being the guiding standard.
A New Hope for Liquid Biopsies: Early Detection of Pancreatic Cancer By Means of Protease Activity Detection in Serum Applying a Hierarchical Decision Structure
Authors: Covarrubias-Zambrano Obdulia , Agarwal Deepesh , Kalubowilage Madumali , Ehsan Sumia , Yapa Asanka S. , Covarrubias Jose , Kasi Anup , Natarajan Balasubramaniam , Bossmann Stefan H.
Published: October 2022

Over the last 6 years, five-year survival rate for pancreatic cancer patients has increased from 6 to 10% after the initial diagnosis, which makes it one of the deadliest cancer types. This disease is known as the “silent killer” because early detection is challenging due to the location of the pancreas in the body and the nonspecific clinical symptoms. The Bossmann group has developed ultrasensitive nanobiosensors for protease/arginase detection comprised of Fe/Fe3O4nanoparticles, cyanine 5.5, and designer peptide sequences linked to TCPP. Initial data obtained from both gene expression analysis and protease/arginase activity detection in serum indicated the feasibility of early pancreatic cancer detection. Several matrix metalloproteinases (MMPs, -1, -3, and -9), cathepsins (CTS) B and E, neutrophil elastase, and urokinase plaminogen activator (uPA) have been identified as candidates for proximal biomarkers. In this study, we have confirmed our initial results from 2018 performing serum sample analysis assays using a larger group sample size (n=159), which included localized (n=33) and metastatic pancreatic cancer (n=50), pancreatitis (n=26), and an age-matched healthy control group (n=50). The data obtained from the eight nanobiosensors capable of ultrasensitive protease and arginase activity measurements were analyzed by means of an optimized information fusion-based hierarchical decision structure. This permits the modeling of early-stage detection of pancreatic cancer as a multi-class classification problem. The most striking result is that this methodology permits the detection of localized pancreatic cancers from serum analyses with 96% accuracy.
The predictive value of renal resistance index and plasma cystatin C in pregnancy-related acute kidney injury
Authors: Tian Suochen , Chang Zhenqin , Wang Qiang , Wu Min , Xu Zhiping , Tian Longying , Sui Yuanda , Cui Yujing , Tian Hui , Zou Xiuli , Liu Mingxin , Wu Tiejun
Published: October 2022

Objective

To analyze the predictive value of renal resistance index (RRI) and plasma cystatin C (pCysC) in pregnancy-related acute kidney injury (PR-AKI).

Methods

This study included 182 pregnant women admitted to the intensive care unit (ICU) between May 2016 and June 2021. Intensivists who had received full-time bedside ultrasound Doppler training performed RRI measurements, and blood was drawn to monitor serum creatinine (Scr) and pCysC concentrations. The study continued for 3 consecutive days, marked as the first day, the second day, and the third day, during which the hourly urine output (UO) was monitored and recorded. According to the AKI diagnostic staging criteria, patients with AKI were divided into stages I, II, and III and comprised the study group (Group A), and patients without AKI served as the control group (Group B).

Results

Of the 182 enrolled patients, 35 (19.2%) were diagnosed with AKI, including 23 (65.7%) with stage I, 9 with stage II (25.7%), and 3 with stage III (8.6%). Three were excluded owing to the requirement of continuous blood purification. Therefore, 179 patients, 32 in Group A and 147 in Group B, were included. The Scr, pCysC, and RRI of Group A increased on the first, second, and third days, but there was a gradual decrease over time. Each period was compared with the corresponding period in Group B, and there were significant differences (P<0.05). All patients in Group A met the diagnostic criterion of Scr concentration in AKI, and only 34.4% of the patients met the diagnostic criterion of UO. According to the D1 monitoring results, the proportions of increased pCysC and RRI in Group A were 87.5% and 81.3%, respectively. They were significantly different from those in Group B (P<0.001). The three variables of pCysC, RRI, and the combination of pCysC and RRI all independently correlated with AKI. The sensitivity and specificity of pCysC concentration for the prediction of PR-AKI were 87.5% and 84.35%, respectively, and those of RRI were 81.25% and 76.87%, respectively. The sensitivity and specificity of the combination of the two were 96.88% and 72.11%, respectively. Receiver operating characteristic curve analysis showed that these indicators had a significant predictive power for PR-AKI. Although the length of stay in the ICU and hospital in Group A was longer (P<0.05), there was no difference in hospital mortality between the two groups (P>0.05).

Conclusion

The diagnosis of PR-AKI based only on Scr and UO was insufficient. RRI and pCysC were important supplements for diagnosing PR-AKI, with good sensitivity and specificity. However, combining the two was better.
Abnormal renal function tests at presentation in severe COVID 19 pneumonia and its effect on clinical outcomes
Authors: Hanif Mehak , Sumalani Kamran Khan , Mandhan Vishal , Shaikh Zarkesh , Haider Shahbaz
Published: October 2022

Aim

To determine the incidence of abnormal renal function tests at presentation in South Asian patients admitted with severe COVID 19 pneumonia and determine its effect on disease severity and clinical outcomes

Methods

This was a retrospective cross-sectional study conducted at the COVID Intensive care unit of a large tertiary care government hospital in Karachi, Pakistan. 190 patients admitted over five months from 1/5/2021 till 30/6/2021 were included in the study. Patient demographic characteristics, comorbidities, and clinical manifestations of COVID 19 infection were recorded. Laboratory values at the time of presentation, including Hemoglobin, NLR, platelets, blood urea nitrogen, glomerular filtration rate (GFR), inflammatory markers, liver function tests, and electrolytes were recorded. Patient outcome and need for mechanical ventilation were assessed 28 days after admission and compared with the incidence of abnormal renal functions at presentation.

Results

Mean GFR and BUN at presentation were 69.7 and 28.4 respectively. 109 (50.4%) patients had abnormal renal function tests at the time of presentation. 76 (40.0%) patients had low GFR and 33 (17.4%) had only raised BUN with normal GFR. Mean GFR was lower in non-survivors vs survivors (p-value 0.000) and in patients who required mechanical ventilation (p-value 0.008). Patients who had low GFR showed greater mortality than those with normal GFR (p-value 0.04) and were more likely to require mechanical ventilation (p-value 0.04).

Conclusion

Low GFR at presentation is common in patients with severe COVID 19 pneumonia and is associated with a higher in-hospital mortality rate and need for mechanical ventilation.
Mechanism of targeted killing of P. aeruginosa by pyocins SX1 and SX2
Authors: Premsuriya Jiraphan , Mosbahi Khedidja , Atanaskovic Iva , Kleanthous Colin , Walker Daniel
Published: October 2022

Pseudomonas aeruginosais a common cause of serious hospital-acquired infections, the leading proven cause of mortality in people with cystic fibrosis and is associated with high levels of antimicrobial resistance. Pyocins are narrow spectrum protein antibiotics produced byP. aeruginosathat kill strains of the same species and have the potential to be developed as therapeutics targeting multi-drug resistant isolates. We have identified two novel pyocins designated SX1 and SX2. Pyocin SX1 is a metal-dependent DNase while pyocin SX2 kills cells through inhibition of protein synthesis. Mapping the uptake pathways of SX1 and SX2 shows these pyocins utilize a combination of the common polysaccharide antigen (CPA) and a previously uncharacterized TonB-dependent transporter (TBDT) PA0434 to traverse the outer membrane. In addition, TonB1 and FtsH are required by both pyocins to energise their transport into cells and catalyse their translocation across the inner membrane, respectively. Expression ofPA0434was found to be specifically regulated by copper availability and we have designated PA0434 as Copper Responsive Transporter A, or CrtA. To our knowledge these are the first S-type pyocins described that utilize a TBDT that is not involved in iron uptake.
Evaluating metabolic and genomic data for predicting grain traits under high night temperature stress in rice
Authors: Bi Ye , Yassue Rafael Massahiro , Paul Puneet , Dhatt Balpreet Kaur , Sandhu Jaspreet , Do Thi Phuc , Walia Harkamal , Obata Toshihiro , Morota Gota
Published: October 2022

The asymmetric increase in average nighttime temperatures relative to increase in average daytime temperatures due to climate change is decreasing grain yield and quality in rice. Therefore, a better understanding of the impact of higher night temperature on single grain at whole genome level is essential for future development of more resilient rice. We investigated the utility of metabolites obtained from grains to classify high night temperature conditions of genotypes, and metabolites and single nucleotide polymorphisms to predict grain length, width, and perimeter phenotypes using a rice diversity panel. We found that the metabolic profiles of rice genotypes alone could be used to classify control and high night temperature conditions with high accuracy using random forest or extreme gradient boosting. The best linear unbiased prediction and BayesC showed greater metabolic prediction performance than machine learning models for grain-size phenotypes. Metabolic prediction was most effective for grain width, resulting in the highest prediction performance. Genomic prediction performed better than metabolic prediction. Integrating metabolites and genomics simultaneously in a prediction model slightly improved prediction performance. We did not observe a difference in prediction between the control and high night temperature conditions. Several metabolites were identified as auxiliary phenotypes that could be used to enhance the multi-trait genomic prediction of grain-size phenotypes. Our results showed that, in addition to single nucleotide polymorphisms, metabolites collected from grains offer rich information to perform predictive analyses, including classification modeling of high night temperature responses and regression modeling of grain size-related phenotypes in rice.
Flux estimation analysis systematically characterizes the metabolic shifts of the central metabolism pathway in human cancer
Authors: Yang Grace , Huang Shaoyang , Hu Kevin , Lu Alex , Yang Jonathan , Meroueh Noah , Dang Pengtao , Zhu Haiqi , Cao Sha , Zhang Chi
Published: October 2022

Glucose and glutamine are major carbon and energy sources that promote the fast proliferation of cancer cells. Metabolic shifs observed on cell line or mouse models may not reflect the general metabolic shifts in real human cancer tissue. In this study, we conducted a computational characterization of the flux distribution and variations of the central energy metabolism and key branches in a pan-cancer analysis, including glycolytic pathway, production of lactate, TCA cycle, nucleic acids synthesis, glutaminolysis, glutaminate, glutamine and glutathione metabolism, amino acids synthesis, in 11 cancer subtypes and 9 matched adjacent normal tissue types, by using TCGA tissue transcriptomics data. Our analysis confirms the increased influx in glucose uptake and glycolysis and decreased upper part of TCA cycle, i.e., Warbug effect in the analyzed cancer types. However, consistently increased lactate production and second half of TCA cycle were only seen in certain cancer types. More interestingly, we did not see cancer tissues have highly shifted glutaminolysis compared to their adjacent normal controls. A systems biology model of metabolic shifts in through cancer and tissue types is further developed and analyzed. We observed that (1) normal tissues have distinct metabolic phenotypes, (2) cancer types have drastically different metabolic shifts compared to their adjacent normal controls, and (3) the different shifts happened to tissue specific metabolic phenotypes result in a converged metabolic phenotype through cancer types and cancer progression. This study strongly suggests the possibility to have a unified framework for studies of cancer-inducing stressors, adaptive metabolic reprogramming, and cancerous behaviors.