bluuebunny/crossref_metadata_2025 huggingface dataset:
Bulk Compositional Influence on Diverse Metapelitic Mineral Assemblages in the Whetstone Lake Area, Ontario
Authors: Forshaw Jacob B , Pattison David RM
Published: September 2023

Understanding the interplay between bulk composition and metamorphic grade underpins our interpretations of metamorphism in orogenic belts. The focus of this study is the regional garnet–staurolite–kyanite–sillimanite metamorphic sequence of the Whetstone Lake area, southeastern Ontario. In the kyanite and lower sillimanite zones of this area, there is exceptional diversity in metapelitic mineral assemblages that cannot be accounted for by differences in metamorphic grade. We present a data set of petrographic observations, phase proportions, whole-rock geochemical compositions, and mineral compositions, from thirty-two samples that encapsulate the range of assemblages found in these zones. Differences in bulk composition are the primary control on mineral assemblage development. Whole-rock XMg = molar MgO/(MgO + FeO) and ${\textrm{X}}_{\textrm{Fe}^{3+}}=\kern0.5em \textrm{molar}\ 2\times{\textrm{Fe}}_2{\textrm{O}}_3/\left(2\times{\textrm{Fe}}_2{\textrm{O}}_3+\textrm{FeO}\right)$ exert the greatest control on the observed mineral assemblages, whilst variation in MnO, K2O, and Al2O3 have a secondary influence. We use a set of quality factors ( Duesterhoeft & Lanari, 2020) to test the ability of thermodynamic models to reproduce the observed mineral assemblages, modal abundances, and mineral compositions in the diverse bulk compositions at Whetstone Lake. Eight samples were selected for phase equilibrium modelling, for which two bulk compositions were calculated for each sample: (1) a whole-rock bulk composition based on an X-ray fluorescence analysis and (2) a carefully considered local bulk composition based on combining mineral proportions with representative mineral compositions, as obtained from a single thin section. Our modelling uses thermodynamic data set 6.2 ( Holland & Powell, 2011) and the solution models of White et al. (2014a, 2014b) that incorporate several Fe3+ end members needed to model the natural data. Modelling in both types of bulk composition broadly predicted mineral assemblages that match those observed. In addition, predicted mineral assemblage fields overlap within uncertainty between 620°C and 675°C and between 6.5 and 7.5 kbar, consistent with the limited range of grade represented by the natural rocks. Predicted modal abundances better match those observed when phase diagrams are constructed using local bulk compositions compared to whole-rock bulk compositions. Despite the acceptable agreement between predicted and observed mineral assemblages, consistent discrepancies are found between predicted and observed mineral compositions. These include overestimation of ${\textrm{X}}_{\textrm{Mg}}^{\ast }$ in garnet, staurolite, and cordierite, overestimation of Ti in staurolite and biotite, underestimation of Si in biotite, and overestimation of Al and underestimation of Fe3+, Fe2+, and Mg in muscovite. The Whetstone Lake suite of this study will be useful to test the predictive capability of future thermodynamic models.
Maize MITOGEN-ACTIVATED PROTEIN KINASE 20 mediates high-temperature–regulated stomatal movement
Authors: Cheng Chuang , Wu Qiqi , Wang Mei , Chen Donghua , Li Jie , Shen Jianlin , Hou Shuguo , Zhang Pengcheng , Qin Li , Acharya Biswa R , Lu Xiaoduo , Zhang Wei
Published: September 2023

High temperature induces stomatal opening; however, uncontrolled stomatal opening is dangerous for plants in response to high temperature. We identified a high-temperature sensitive (hts) mutant from the ethyl methane sulfonate (EMS)-induced maize (Zea mays) mutant library that is linked to a single base change in MITOGEN-ACTIVATED PROTEIN KINASE 20 (ZmMPK20). Our data demonstrated that hts mutants exhibit substantially increased stomatal opening and water loss rate, as well as decreased thermotolerance, compared to wild-type plants under high temperature. ZmMPK20-knockout mutants showed similar phenotypes as hts mutants. Overexpression of ZmMPK20 decreased stomatal apertures, water loss rate, and enhanced plant thermotolerance. Additional experiments showed that ZmMPK20 interacts with MAP KINASE KINASE 9 (ZmMKK9) and E3 ubiquitin ligase RPM1 INTERACTING PROTEIN 2 (ZmRIN2), a maize homolog of Arabidopsis (Arabidopsis thaliana) RIN2. ZmMPK20 prevented ZmRIN2 degradation by inhibiting ZmRIN2 self-ubiquitination. ZmMKK9 phosphorylated ZmMPK20 and enhanced the inhibitory effect of ZmMPK20 on ZmRIN2 degradation. Moreover, we employed virus-induced gene silencing (VIGS) to silence ZmMKK9 and ZmRIN2 in maize and heterologously overexpressed ZmMKK9 or ZmRIN2 in Arabidopsis. Our findings demonstrated that ZmMKK9 and ZmRIN2 play negative regulatory roles in high-temperature–induced stomatal opening. Accordingly, we propose that the ZmMKK9–ZmMPK20–ZmRIN2 cascade negatively regulates high-temperature–induced stomatal opening and balances water loss and leaf temperature, thus enhancing plant thermotolerance.
The impact of current and future climates on spatiotemporal dynamics of influenza in a tropical setting
Authors: Mahmud Ayesha S , Martinez Pamela P , Baker Rachel E
Published: September 2023

Although the drivers of influenza have been well studied in high-income settings in temperate regions, many open questions remain about the burden, seasonality, and drivers of influenza dynamics in the tropics. In temperate climates, the inverse relationship between specific humidity and transmission can explain much of the observed temporal and spatial patterns of influenza outbreaks. Yet, this relationship fails to explain seasonality, or lack there-of, in tropical and subtropical countries. Here, we analyzed eight years of influenza surveillance data from 12 locations in Bangladesh to quantify the role of climate in driving disease dynamics in a tropical setting with a distinct rainy season. We find strong evidence for a nonlinear bimodal relationship between specific humidity and influenza transmission in Bangladesh, with highest transmission occurring for relatively low and high specific humidity values. We simulated influenza burden under current and future climate in Bangladesh using a mathematical model with a bimodal relationship between humidity and transmission, and decreased transmission at very high temperatures, while accounting for changes in population immunity. The climate-driven mechanistic model can accurately capture both the temporal and spatial variation in influenza activity observed across Bangladesh, highlighting the usefulness of mechanistic models for low-income countries with inadequate surveillance. By using climate model projections, we also highlight the potential impact of climate change on influenza dynamics in the tropics and the public health consequences.
Non-symmetric responses of leaf onset date to natural warming and cooling in northern ecosystems
Authors: He Lei , Wang Jian , Ciais Philippe , Ballantyne Ashley , Yu Kailiang , Zhang Wenxin , Xiao Jingfeng , Ritter François , Liu Zhihua , Wang Xufeng , Li Xiaojun , Peng Shouzhang , Ma Changhui , Zhou Chenghu , Li Zhao-Liang , Xie Yaowen , Ye Jian-Sheng
Published: September 2023

The northern hemisphere has experienced regional cooling, especially during the global warming hiatus (1998–2012) due to ocean energy redistribution. However, the lack of studies about the natural cooling effects hampers our understanding of vegetation responses to climate change. Using 15,125 ground phenological time series at 3,620 sites since the 1950s and 31-year satellite greenness observations (1982–2012) covering the warming hiatus period, we show a stronger response of leaf onset date (LOD) to natural cooling than to warming, i.e. the delay of LOD caused by 1°C cooling is larger than the advance of LOD with 1°C warming. This might be because cooling leads to larger chilling accumulation and heating requirements for leaf onset, but this non-symmetric LOD response is partially offset by warming-related drying. Moreover, spring greening magnitude, in terms of satellite-based greenness and productivity, is more sensitive to LOD changes in the warming area than in the cooling. These results highlight the importance of considering non-symmetric responses of spring greening to warming and cooling when predicting vegetation-climate feedbacks.
Eviction and Poverty in American Cities
Authors: Collinson Robert , Humphries John Eric , Mader Nicholas , Reed Davin , Tannenbaum Daniel , van Dijk Winnie
Published: September 2023

More than two million U.S. households have an eviction case filed against them each year. Policy makers at the federal, state, and local levels are increasingly pursuing policies to reduce the number of evictions, citing harm to tenants and high public expenditures related to homelessness. We study the consequences of eviction for tenants using newly linked administrative data from two major urban areas: Cook County (which includes Chicago) and New York City. We document that before housing court, tenants experience declines in earnings and employment and increases in financial distress and hospital visits. These pre trends pose a challenge for disentangling correlation and causation. To address this problem, we use an instrumental variables approach based on cases randomly assigned to judges of varying leniency. We find that an eviction order increases homelessness and hospital visits and reduces earnings, durable goods consumption, and access to credit in the first two years. Effects on housing and labor market outcomes are driven by effects for female and Black tenants. In the longer run, eviction increases indebtedness and reduces credit scores.
Do the features of juvenile psoriatic arthritis change according to age? A comprehensive evaluation of the PeRA Research Group Registry
Authors: Karadağ Şerife Gül , Coskuner Taner , Demirkan Fatma Gül , Sonmez Hafize Emine , Ozdel Semanur , Çakan Mustafa , Otar Yener Gulcin , Ozturk Kubra , Demir Ferhat , Sozeri Betül , Aktay Ayaz Nuray
Published: September 2023

Objectives

To describe the clinical features and treatment outcomes of children with juvenile psoriatic arthritis (JPsA) and compare the distinct patterns of the disease between early-onset and late-onset age groups.

Methods

Patients with JPsA followed regularly for at least 6 months between 2010 and 2020 in seven paediatric rheumatology centres in Turkey were included in the study. The demographic features, clinical manifestations, treatment strategies and outcomes of the patients were evaluated retrospectively.

Results

A total of 87 (46 male/41 female) patients were included in the study. The mean age at diagnosis was 11.9 years (s.d. 4.5). Fifty-seven (65.5%) patients had psoriasis at the time of diagnosis and arthritis preceded psoriasis in 10 (11.5%) patients. Thirty (34.5%) patients had dactylitis, 28 (32.2%) had nail pitting, 36 (41.4%) had involvement of the small joints and 20 (23%) had enthesitis. Sacroiliitis was detected in 11 (12.6%) patients by MRI. ANA was positive in 35 (40.2%) patients. Twelve children (13.8%) were in the early-onset (<5 years) group. Uveitis and ANA positivity were more common in the early-onset group. Active joint counts and activity scores of our patients showed significant improvement at month 6 and at the last control compared with baseline.

Conclusion

About one-third of patients with JPsA do not have psoriasis at the time of diagnosis. In some patients, no skin lesion is seen during the course of the disease. Children with PsA seem to display two different phenotypes. Younger children have a female predominance, ANA positivity and uveitis, while older children have more axial involvement.
Opposing Effects on Descending Control of Nociception by µ and κ Opioid Receptors in the Anterior Cingulate Cortex
Authors: Navratilova Edita , Qu Chaoling , Ji Guangchen , Neugebauer Volker , Guerrero Miguel , Rosen Hugh , Roberts Edward , Porreca Frank
Published: September 2023

Background

The efficiency of descending pain modulation, commonly assessed with the conditioned pain modulation procedure, is diminished in patients with chronic pain. The authors hypothesized that the efficiency of pain modulation is controlled by cortical opioid circuits.

Methods

This study evaluated the effects of µ opioid receptor activation in the anterior cingulate cortex on descending control of nociception, a preclinical correlate of conditioned pain modulation, in male Sprague-Dawley rats with spinal nerve ligation–induced chronic pain or in sham-operated controls. Additionally, the study explored the consequences of respective activation or inhibition of κ opioid receptor in the anterior cingulate cortex of naive rats or animals with neuropathic pain. Descending control of nociception was measured as the hind paw withdrawal response to noxious pressure (test stimulus) in the absence or presence of capsaicin injection in the forepaw (conditioning stimulus).

Results

Descending control of nociception was diminished in the ipsilateral, but not contralateral, hind paw of rats with spinal nerve ligation. Bilateral administration of morphine in the anterior cingulate cortex had no effect in shams but restored diminished descending control of nociception without altering hypersensitivity in rats with neuropathic pain. Bilateral anterior cingulate cortex microinjection of κ opioid receptor antagonists, including nor-binaltorphimine and navacaprant, also re-established descending control of nociception in rats with neuropathic pain without altering hypersensitivity and with no effect in shams. Conversely, bilateral injection of a κ opioid receptor agonist, U69,593, in the anterior cingulate cortex of naive rats inhibited descending control of nociception without altering withdrawal thresholds.

Conclusions

Anterior cingulate cortex κ opioid receptor activation therefore diminishes descending control of nociception both in naive animals and as an adaptive response to chronic pain, likely by enhancing net descending facilitation. Descending control of nociception can be restored by activation of μ opioid receptors in the anterior cingulate cortex, but also by κ opioid receptor antagonists, providing a nonaddictive alternative to opioid analgesics. Navacaprant is now in advanced clinical trials.

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New
Diagnostic Accuracy of Smartphone Corneal Photography for Detection of Corneal Opacities in a Resource-Limited Setting: A Community-Based Study
Authors: Cao Binh , Giri Puspa , Byanju Raghunandan , Pradhan Sangita , Bhandari Gopal , Bhandari Sadhan , Kandel Ram Prasad , Poudyal Bimal , Gonzales John A. , Srinivasan Muthiah , Upadhyay Madan , Whitcher John P. , O'Brien Kieran S. , Lietman Thomas M. , Keenan Jeremy D.
Published: September 2023

Purpose:

To evaluate the diagnostic accuracy of smartphone corneal photography in detecting corneal opacities in a community-based setting.

Methods:

A case-control, diagnostic accuracy study was nested in a cluster-randomized trial of a corneal ulcer prevention intervention in Nepal. Smartphone corneal photography was performed annually on community members self-reporting a potential risk factor for a corneal infection. Corneal photographs were graded for the presence or absence of an opacity. All cases with an opacity on smartphone photography and an equal number of controls were invited for a comprehensive eye examination with a slit lamp biomicroscope at an eye hospital. A mobile team visited participants unable to come to the hospital, conducting a limited examination with a penlight.

Results:

Of 1332 study participants (666 cases and 666 controls), 1097 had a penlight examination (535 cases and 562 controls) and 191 had a slit lamp examination (120 cases and 71 controls). When penlight examination was considered the reference standard, smartphone diagnosis of a corneal opacity had a positive predictive value (PPV) of 47% (95% confidence interval 43%–52%) and negative predictive value (NPV) of 95% (93%–97%). When slit lamp examination was considered the reference standard, the overall PPV and NPV were 71% (62%–78%) and 80% (70%–88%), respectively. The NPV was greater for detection of opacities >1 mm, estimated at 95% (90%–98%).

Conclusions:

Corneal photography performed in a resource-limited community-based setting using a smartphone coupled to an external attachment had acceptable diagnostic accuracy for detection of corneal opacities large enough to be clinically meaningful.
RNA nanomedicine in liver diseases
Authors: Bakrania Anita , Mo Yulin , Zheng Gang , Bhat Mamatha
Published: September 2023

The remarkable impact of RNA nanomedicine during the COVID-19 pandemic has demonstrated the expansive therapeutic potential of this field in diverse disease contexts. In recent years, RNA nanomedicine targeting the liver has been paradigm-shifting in the management of metabolic diseases such as hyperoxaluria and amyloidosis. RNA nanomedicine has significant potential in the management of liver diseases, where optimal management would benefit from targeted delivery, doses titrated to liver metabolism, and personalized therapy based on the specific site of interest. In this review, we discuss in-depth the different types of RNA and nanocarriers used for liver targeting along with their specific applications in metabolic dysfunction-associated steatotic liver disease, liver fibrosis, and liver cancers. We further highlight the strategies for cell-specific delivery and future perspectives in this field of research with the emergence of small activating RNA, circular RNA, and RNA base editing approaches.
Bile acid–induced IRF3 phosphorylation mediates cell death, inflammatory responses, and fibrosis in cholestasis-induced liver and kidney injury via regulation of ZBP1
Authors: Zhuang Yuan , Ortega-Ribera Martí , Thevkar Nagesh Prashanth , Joshi Radhika , Huang Huihui , Wang Yanbo , Zivny Adam , Mehta Jeeval , Parikh Samir M. , Szabo Gyongyi
Published: September 2023

Background and Aims:

Cell death and inflammation play critical roles in chronic tissue damage caused by cholestatic liver injury leading to fibrosis and cirrhosis. Liver cirrhosis is often associated with kidney damage, which is a severe complication with poor prognosis. Interferon regulatory factor 3 (IRF3) is known to regulate apoptosis and inflammation, but its role in cholestasis remains obscure. In this study.

Approach and Results:

We discovered increased IRF3 phosphorylation in the liver of patients with primary biliary cholangitis and primary sclerosing cholangitis. In the bile duct ligation model of obstructive cholestasis in mice, we found that tissue damage was associated with increased phosphorylated IRF3 (p-IRF3) in the liver and kidney. IRF3 knockout (Irf3

−/−
) mice showed significantly attenuated liver and kidney damage and fibrosis compared to wide-type mice after bile duct ligation. Cell-death pathways, including apoptosis, necroptosis, and pyroptosis, inflammasome activation, and inflammatory responses were significantly attenuated in Irf3
−/− mice. Mechanistically, we show that bile acids induced p-IRF3 in vitro in hepatocytes. In vivo, activated IRF3 positively correlated with increased expression of its target gene, Z-DNA–Binding Protein-1 (ZBP1), in the liver and kidney. Importantly, we also found increased ZBP1 in the liver of patients with primary biliary cholangitis and primary sclerosing cholangitis. We discovered that ZBP1 interacted with receptor interacting protein 1 (RIP1), RIP3, and NLRP3, thereby revealing its potential role in the regulation of cell-death and inflammation pathways. In conclusion.

Conclusions:

Our data indicate that bile acid–induced p-IRF3 and the IRF3-ZBP1 axis play a central role in the pathogenesis of cholestatic liver and kidney injury.
Vegetarian diets and the risk of gastrointestinal cancers: a meta-analysis of observational studies
Authors: Bai Tongtong , Peng Juanjuan , Zhu Xinqi , Wu Chengyu
Published: September 2023

The systematic review aimed to assess the association between vegetarian diet and the risk of gastrointestinal tumorigenesis. PubMed, Embase, Cochrane Library, and Web of Science were searched from inception to August 2022 for observational studies on vegetarian diets and the risk of gastrointestinal tumorigenesis. The primary outcome was morbidity due to gastrointestinal cancer. The Newcastle-Ottawa Scale was used to assess the quality of included studies. Pooled effects were analyzed using a random-effects model. The study protocol was registered in PROSPERO (no. CRD42022310187). Eight original studies (seven cohorts and one case-control), involving 686 691 participants, were included. Meta-analysis showed a negative correlation between vegetarian diets and gastrointestinal tumorigenesis risk [relative risk (RR) equals 0.77, 95% confidence interval (CI) is (0.65–0.90)], compared with non-vegetarian diets. Subgroup analysis indicated that vegetarian diets were negatively correlated with the risks of gastric cancer [RR = 0.41, 95% CI (0.28–0.61)] and colorectal cancer [RR = 0.85, 95% CI (0.76–0.95)], but not with that of upper gastrointestinal cancer (excluding stomach) [RR = 0.93, 95% CI (0.61–1.42)]. Vegetarian diets were negatively correlated with the risk of gastrointestinal tumorigenesis in men [RR = 0.57, 95% CI (0.36–0.91)], but were uncorrelated in women [RR = 0.89, 95% CI (0.71–1.11)]. Vegetarian diets were negatively correlated with the risk of gastrointestinal tumorigenesis in North American [RR = 0.76, 95% CI (0.61–0.95)] and Asian populations [RR = 0.43, 95% CI (0.26–0.72)] and were uncorrelated in the European population [RR = 0.83, 95% CI (0.68–1.01)]. Adhering to vegetarian diets reduces the risk of gastrointestinal tumorigenesis. More data from well-conducted cohort and other studies are needed.
Unveiling the growing significance of metabolism in modulating immune cell function: exploring mechanisms and implications; a review
Authors: Aderinto Nicholas , Abdulbasit Muili Opeyemi , Tangmi Adrien Djabo Eric , Okesanya John Olalekan , Mubarak Jolayemi Mustapha
Published: September 2023

Immunometabolism has emerged as a rapidly growing field of research, holding significant promise for personalised medicine and precision immunotherapy. This review explores the intricate relationship between immune function and metabolic processes, emphasising their profound impact on various immune-related disorders. Understanding how metabolic dysregulation contributes to the pathogenesis of these disorders remains a critical research gap. Therefore, this review aims to bridge that gap by examining the key metabolic pathways involved and their specific implications in immune cell function. Key metabolic pathways, including glycolysis, mitochondrial metabolism, fatty acid metabolism, and amino acid metabolism, are discussed in the context of immune cell function. Dysregulation of these pathways can disrupt immune cell activation, differentiation, and overall function, contributing to disease pathogenesis. Understanding these metabolic alterations’ molecular mechanisms is essential for developing targeted therapeutic interventions. The review also emphasises the importance of personalised medicine in immune-related disorders. The unique metabolic profiles of individuals can influence treatment outcomes, highlighting the need for tailored approaches. Integrating metabolic profiling into clinical practice can enhance treatment efficacy and improve patient outcomes. Investigating the clinical significance of immunometabolism in diverse disease contexts will facilitate the translation of research findings into clinical practice. Moreover, refining treatment strategies based on individual metabolic profiles will contribute to advancing precision immunotherapy.
Two years of COVID-19 vaccination in Nigeria: a review of the current situation of the pandemic: a literature review
Authors: Ogunniyi Tolulope Joseph , Rufai Basirat Oluwadamilola , Uketeh Sunday Nguher , Turzin Justice Kwadwo , Oyinloye Emmanuel Abiodun , Effiong Fortune Benjamin
Published: September 2023

Curtailing COVID-19 outbreaks has been the major focus for many countries following the onset of the COVID-19 pandemic. Nigeria expanded its effort with the commencement of its vaccination program against COVID-19 in March 2021 after several less effective interventions as vaccine introduction was implemented. Following the introduction of the vaccines, Nigeria is expected to meet the worldwide COVID-19 eradication target of vaccinating 40% and 70% of the population, respectively, by the end of 2021 and 2022. Nigeria was unable to meet the target at the commencement of the program. The low vaccination rate, attributed to a low acceptance rate of vaccines, a lack of access to vaccines, poor communication, a weak cold-chain system, and inadequate infrastructure in the country, resulted in the complete vaccination of only 15% of the Nigerian populace as of 21 September 2022. To improve the vaccination rate, the COVID-19 Crisis Communication Centre was launched. Also, the implementation of delivery of service, logistics, accountability, supportive supervision, communication, and electronic management of immunization data scaled the vaccination rate to more than 54% of the target populace as of December 2022. Since the introduction of the COVID-19 vaccine, a substantial change in the prevalence and mortality rate has been perceived owing to the country’s progress toward achieving herd immunity against COVID-19. The country ascertained the percentage of cumulative deaths before the vaccination process to be 60.4%, which was reduced to 39.6% post-vaccination. In comparison, the percentage of confirmed COVID-19 cases was reduced from 58.3 to 41.7% post-vaccination. The authors recommend that the government and relevant public health authorities ensure meticulous documentation of the outcomes resulting from vaccination initiatives and facilitate the accessibility of this information to the general public to boost the vaccination rate.
Research frontiers and hotspots in bacterial biofilm wound therapy: bibliometric and visual analysis for 2012–2022
Authors: Liu Rong , Zhai Linjun , Feng Shengya , Gao Rong , Zheng Jie
Published: September 2023

Background:

Bacterial biofilms, which can protect bacteria from host immune response and drug attack, are an important factor in the difficult healing of chronic wound infection, which has become a major problem in medical development. This paper aimed to analyze literature related to bacterial biofilm wound treatment published between 2012 and 2022 using bibliometric and visual analysis.

Methods:

Publications related to bacterial biofilm wound treatment from 2012 to 2022 were selected from the Web of Science Core Collection. Microsoft Excel 2021, bibliometrics, CiteSpace6.1, and VOSviewer1.6.18 were used to extract and analyze data.

Results:

A total of 940 articles were published between 2012 and 2022, with the United States being the leading country (with 302 papers, 32.13%) and the University of Copenhagen in Denmark being the leading institution (with 26 published articles) in the field. Steven L Percival, a British academic, published the most articles (14). In the field of bacterial biofilm wound treatment, keywords suggested that the research gradually transitioned from lower limb venous ulcer, negative pressure-assisted healing to chronic wound, in-vitro bacterial biological model research, and then to the development of more microscopic and more advanced technologies such as antibacterial activity and nanomaterials. “Nanoparticles”, “inhibition/antibacterial”, “delivery”, “gold nanoparticles”, “hydrogel”, “wound healing”, etc., may become new research hotspots in this field.

Conclusion:

There is a lack of specific and effective treatment methods for diagnosing and treating bacterial biofilms in wounds. Through the development of multidisciplinary cooperation, early diagnosis and treatment of bacterial biofilms in wounds can be achieved. These data may provide a useful reference for scholars studying more effective bacterial biofilm wound treatment.
Expanding Access to Organ Transplant for People Living With HIV: Can Policy Catch Up to Outcomes Data?
Authors: Chandran Sindhu , Stock Peter G. , Roll Garrett R.
Published: September 2023

Advances in antiretroviral and immunosuppressive regimens have improved outcomes following solid organ transplantation in people living with HIV (PLWH). The HIV Organ Policy and Equity Act was conceived to reduce the discard of HIV-positive organs and improve access to transplant for PLWH. Nevertheless, PLWH continue to experience disproportionately low rates of transplant. This overview examines the hurdles to transplantation in PLWH with end-organ disease, the potential and realized impact of the HIV Organ Policy and Equity Act, and changes that could permit expanded access to organ transplant in this population.
Migration and differentiation of muscle stem cells are coupled by RhoA signalling during regeneration
Authors: Brondolin Mirco , Herzog Dylan , Sultan Sami , Warburton Fiona , Vigilante Alessandra , Knight Robert D.
Published: September 2023

Skeletal muscle is highly regenerative and is mediated by a population of migratory adult muscle stem cells (muSCs). Effective muscle regeneration requires a spatio-temporally regulated response of the muSC population to generate sufficient muscle progenitor cells that then differentiate at the appropriate time. The relationship between muSC migration and cell fate is poorly understood and it is not clear how forces experienced by migrating cells affect cell behaviour. We have used zebrafish to understand the relationship between muSC cell adhesion, behaviour and fatein vivo. Imaging of pax7-expressing muSCs as they respond to focal injuries in trunk muscle reveals that they migrate by protrusive-based means. By carefully characterizing their behaviour in response to injury we find that they employ an adhesion-dependent mode of migration that is regulated by the RhoA kinase ROCK. Impaired ROCK activity results in reduced expression of cell cycle genes and increased differentiation in regenerating muscle. This correlates with changes to focal adhesion dynamics and migration, revealing that ROCK inhibition alters the interaction of muSCs to their local environment. We propose that muSC migration and differentiation are coupled processes that respond to changes in force from the environment mediated by RhoA signalling.
Nasopharyngeal carriage rate, serotype distribution, and antimicrobial profiles of Streptococcus pneumoniae among patients with acute respiratory tract infection in Manado, North Sulawesi, Indonesia
Authors: Purwanto Diana Shintawati , Khoeri Miftahuddin Majid , Tafroji Wisnu , Margaretha Kaligis Stefana Helena , Wilar Rocky , Kepel Billy Johnson , Raranta Hessyani Patricia Theodora , Gaghiwu Lidia , Hammerschmidt Sven , Ervina Waode Fifin , Safari Dodi
Published: September 2023

We studied the carriage rate, distribution of serotype, and antimicrobial profile of Streptococcus pneumoniae (S. pneumoniae) among patients with acute respiratory tract infections (ARTI) in two primary health centers and a tertiary referral hospital from 2019 to 2020 in Manado, North Sulawesi, Indonesia before 13-valent PCV (PCV13) introduction. One hundred and six of nasopharyngeal swab samples were collected from children and adult patients. Serotyping of S. pneumoniae strain was performed with sequential multiplex PCR and Quellung reaction. Antimicrobial profile was performed by the disk diffusion method. We identified thirty-one patients carried S. pneumoniae strains (29%). The S. pneumoniae carriage rate was found to be higher among children aged 2-5 years (40.6%) than in children under 1 year (29.6%), children and adolescents under 18 years of age (25.0%) and adult patients (18.5%). The distribution of serotypes varied, including 14, 18C, 19A, 23F, 19F and 35B (two strains each) and 1, 3, 6B, 6C, 31, 9V, 15C, 16F, 17F, 23A, and 35F (one strain each). We found S. pneumoniae isolates were susceptible to vancomycin (97%) followed by chloramphenicol (94%), clindamycin (94%), erythromycin (71%), azithromycin (71%), tetracycline (45%), penicillin (35%), and sulfamethoxazole/trimethoprim (32%). This study provides supporting baseline data on distribution of serotype and antimicrobial profile of S. pneumoniae among patients with ARTI before PCV13 introduction in Manado, North Sulawesi, Indonesia.
Five novel Hymenobacter species isolated from air: Hymenobacter cellulosilyticus sp. nov., Hymenobacter cellulosivorans sp. nov., Hymenobacter aerilatus sp. nov., Hymenobacter sublimis sp. nov. and Hymenobacter volaticus sp. nov.
Authors: Kim Yiseul , Subramanian Parthiban , Choi Hyorim , Weon Hang-Yeon , Kim Seunghwan , Kwon Soon-Wo , Lee Daseul , Han Byeong-Hak , Hong Seung-Beom , Heo Jun
Published: September 2023

Five

Hymenobacter

strains isolated from air samples collected from the Suwon and Jeju regions of the Republic of Korea were studied using polyphasic taxonomic methods. Using 16S rRNA gene sequences and the resulting phylogenetic tree, the strains were primarily identified as members of the genus

Hymenobacter

. Digital DNA–DNA hybridization values and average nucleotide identities values for species delineation (70 and 95–96 %, respectively) between the five strains and their nearest type strains indicated that each strain represented a novel species. All strains were aerobic, Gram-stain-negative, mesophilic, rod-shaped and catalase- and oxidase-positive, with red to pink coloured colonies. The genome sizes of the five strains varied from 4.8 to 7.1 Mb and their G+C contents were between 54.1 and 59.4 mol%. Based on their phenotypic, chemotaxonomic and genotypic characteristics, we propose to classify these isolates into five novel species within the genus

Hymenobacter

for which we propose the names, Hymenobacter cellulosilyticus sp. nov., Hymenobacter cellulosivorans sp. nov., Hymenobacter aerilatus sp. nov., Hymenobacter sublimis sp. nov. and Hymenobacter volaticus sp. nov., with strains 5116 S-3T (=KACC 21925T=JCM 35216T), 5116 S-27T (=KACC 21926T=JCM 35217T), 5413 J-13T (=KACC 21928T=JCM 35219T), 5516 S-25T (=KACC 21931T=JCM 35222T) and 5420 S-77T (=KACC 21932T=JCM 35223T) as the type strains, respectively.
A comparative study of the physical and cooking characteristics of
common types of rice collected from the market by quantitative statistical
analysis
Authors: Ilia Evan Butrus , Saleem Mahmood Fadhil , Hassanzadeh Hamed
Published: September 2023

Fifteen types of rice collected from Kurdistan region-Iraq were investigated by
principal component analysis (PCA) in terms of physical properties and cooking
characteristics. The dimensions of evaluated grains correspond to 5.05-8.75 mm
for length, 1.54-2.47 mm for width, and 1.37-1.95 for thickness. The equivalent
diameter was in the range of 5.23-10.03 mm, and the area took 13.30-28.25
mm2. The sphericity analysis values varied from 0.32 to 0.56, the
aspect ratio from 0.17 to 0.39, and the volume of the grain was measured in the
range from 4.48 to 17.74 mm3, hectoliter weight values were 730-820
kg/m3, and true density from 0.6 to 0.96 g/cm3. The
broken grain ratio was 1.5-18.3%, thousand kernel weight corresponded to
15.88 to 22.42 g. The water uptake ratios for 30 min of soaking were increased
at 60°C compared to 30 and 45°C. The PCA was used to study the
correlation of the most effective factors. Results of PCA showed that the first
(PC1) and second (PC2) components retained 63.4% and 34.8% of the
total variance, which PC1 was mostly related to hectoliter, broken ratio, and
moisture content characteristics while PC2 was mostly concerned with hardness
and true density. For cooking properties, the PC1 and PC2 retained 88.5%
and 9.3% of the total variance, respectively. PC1 was mostly related to
viscosity, spring value, and hardness after cooking, while PC2 was mostly
concerned with spring value, hardness before cooking, and hardness after
cooking.
The clinical, genomic, and transcriptomic landscape of BRAF mutant cancers
Authors: Kazandjian Suzanne , Rousselle Emmanuelle , Dankner Matthew , Cescon David W. , Spreafico Anna , Ma Kim , Kavan Petr , Batist Gerald , Rose April A. N.
Published: September 2023

Background

BRAF mutations are classified into 4 molecularly distinct groups, and Class 1 (V600) mutant tumors are treated with targeted therapies. Effective treatment has not been established for Class 2/3 or BRAF Fusions. We investigated whether BRAF mutation class differed according to clinical, genomic, and transcriptomic variables in cancer patients.

Methods

Using the AACR GENIE (v.12) cancer database, the distribution of BRAF mutation class in adult cancer patients was analyzed according to sex, age, primary race, and tumor type. Genomic alteration data and transcriptomic analysis was performed using The Cancer Genome Atlas.

Results

BRAF mutations were identified in 9515 (6.2%) samples among 153,834, with melanoma (31%), CRC (20.7%), and NSCLC (13.9%) being the most frequent cancer types. Class 1 harbored co-mutations outside of the MAPK pathway (TERT, RFN43) vs Class 2/3 mutations (RAS, NF1). Across all tumour types, Class 2/3 were enriched for alterations in genes involved in UV response and WNT/β-catenin. Pathway analysis revealed enrichment of WNT/β-catenin and Hedgehog signaling in non-V600 mutated CRC. Males had a higher proportion of Class 3 mutations vs. females (17.4% vs 12.3% q = 0.003). Non-V600 mutations were generally more common in older patients (aged 60+) vs younger (38% vs 15% p<0.0001), except in CRC (15% vs 30% q = 0.0001). Black race was associated with non-V600 BRAF alterations (OR: 1.58; p<0.0001).

Conclusions

Class 2/3 BRAF are more present in Black, male patients with co-mutations outside of the MAPK pathway, likely requiring additional oncogenic input for tumorigenesis. Improving access to NGS and trial enrollment will help development of targeted therapies for non-V600 BRAF mutations.

Statement of Translational Relevance

BRAF mutations are classified in 4 categories based on molecular characteristics, but only Class 1 BRAF V600 have effective targeted treatment strategies. With increasing access to next-generation sequencing, oncologists are more frequently uncovering non-V600 BRAF mutations, where there remains a scarcity of effective therapies. Responsiveness to MAPK pathway inhibitors differs according to BRAF mutation class and primary tumor type. For this reason, we sought to determine whether key demographic, genomic, and transcriptomic differences existed between classes. This cross-sectional study analyzes the largest dataset of BRAF-mutated cancers to date. Our findings propose insights to optimize clinical trial design and patient selection in the pursuit of developing effective treatment strategies for patients whose tumors harbor non-V600 BRAF mutations. This study also offers insights into the potential of targeting alternative pathways in addition to the MAPK pathway as part of combinatorial treatment strategies.
Specialty Organization Finances and Membership: A Closer Look
Authors: Syed Ali , Rahimy Ehsan , Sridhar Jayanth
Published: September 2023

Background

United States students and physicians face massive financial hurdles including student loan repayments, board certification fees, and other expenses. This project investigates an infrequently discussed topic, the costs to join and the finances of national specialty organizations.

Purpose

We hope our findings encourage resident physicians and newly minted attendings to take interest in the handling of the fees they may pay to join a national organization.

Methods

Publicly available IRS 990 filings and specialty organization websites were examined to compile data regarding membership fees, organization revenue, expenses, and top earner salaries for 29 total specialty organizations. Descriptive and inferential statistics including Pearson correlation coefficients were used to investigate the above data.

Results

The average annual revenue and net assets for the organizations studied were $50,762,279 and $66,444,291, respectively. The average annual membership fee was $542. The largest ratios of membership fee to physician salary were in pediatrics (0.31%) and ophthalmology (0.26%). The average salary of the top three earners at specialty organizations was $429,758.

Conclusions

There is wide variability in the costs of joining medical specialty organizations in the United States that does not correlate with the average earning potential of individual specialties. As a whole, medical specialty organizations should consider greater financial transparency.
AITeQ: A machine learning framework for Alzheimer’s prediction using a distinctive 5-gene signature
Authors: Ahammad Ishtiaque , Lamisa Anika Bushra , Bhattacharjee Arittra , Jamal Tabassum Binte , Arefin Md. Shamsul , Chowdhury Zeshan Mahmud , Hossain Mohammad Uzzal , Das Keshob Chandra , Keya Chaman Ara , Salimullah Md
Published: September 2023

Neurodegenerative diseases, such as Alzheimer’s disease, pose a significant global health challenge with their complex etiology and elusive biomarkers. In this study, we developed the Alzheimer’s Identification Tool using RNA-Seq (AITeQ), a machine learning model based on an optimized random forest algorithm for identification of Alzheimer’s from RNA-Seq data. Analysis of RNA-Seq data from 433 individuals, including 293 Alzheimer’s patients and 140 controls led to the discovery of 47,929 differentially expressed genes. This was followed by a machine learning protocol involving feature selection, model training, performance evaluation, and hyperparameter tuning. The feature selection process undertaken in this study, employing a combination of 4 different methodologies, culminated in the identification of a compact yet impactful set of 5 genes. Ten diverse machine learning models were trained and tested using these 5 genes (ITGA10, CXCR4, ADCYAP1, SLC6A12, VGF). Performance metrics, including precision, recall, F1-score, accuracy, receiver operating characteristic area under the curve, and confusion matrices, were assessed before and after hyperparameter tuning. Overall, the random forest model with optimized hyperparameters was identified as the best and was used to develop AITeQ. AITeQ is available at:https://github.com/ishtiaque-ahammad/AITeQ

Key Points

A set of 5 genes (ITGA10, CXCR4, ADCYAP1, SLC6A12, VGF) were identified following differential gene expression and feature importance analysis.

Ten diverse machine learning algorithms were trained and tested using the gene expression patterns of the identified 5 genes. The random forest algorithm with customized hyperparameters was found to be the best-performing model for differentiating Alzheimer’s disease samples from control.

AITeQ, a user-friendly, reliable, and accurate machine learning framework for Alzheimer’s disease prediction was developed based on the 5 gene signature.
PSICHIC: physicochemical graph neural network for learning protein-ligand interaction fingerprints from sequence data
Authors: Koh Huan Yee , Nguyen Anh T.N. , Pan Shirui , May Lauren T. , Webb Geoffrey I.
Published: September 2023

In drug discovery, determining the binding affinity and functional effects of small-molecule ligands on proteins is critical. Current computational methods can predict these protein-ligand interaction properties but often lose accuracy without high-resolution protein structures and falter in predicting functional effects. We introduce PSICHIC (PhySIcoCHemICal graph neural network), a framework uniquely incorporating physicochemical constraints to decode interaction fingerprints directly from sequence data alone. This enables PSICHIC to attain first-of-its-kind emergent capabilities in deciphering mechanisms underlying protein-ligand interactions, achieving state-of-the-art accuracy and interpretability. Trained on identical protein-ligand pairs without structural data, PSICHIC matched and even surpassed leading structure-based methods in binding affinity prediction. In a library screening for adenosine A1 receptor agonists, PSICHIC discerned functional effects effectively, ranking the sole novel agonist within the top three. PSICHIC’s interpretable fingerprints identified protein residues and ligand atoms involved in interactions. We foresee PSICHIC reshaping virtual screening and deepening our understanding of protein-ligand interactions.
Validation of Dual Energy X-ray Absorptiometry for longitudinal quantification of tumor burden in a murine model of pancreatic ductal adenocarcinoma
Authors: Sechrist Zachary R. , Lee Grace , Schwarz Edward M. , Cole Calvin L.
Published: September 2023

Noninvasive imaging is central to preclinical, in vivo models of pancreatic ductal adenocarcinoma (PDAC). While bioluminescent imaging (BLI) is a gold standard, its signal is dependent on the metabolic activity of tumor cells. In contrast, dual energy X-ray absorptiometry (DEXA) is a direct measure of body composition. Thus, we aimed to assess its potential for longitudinal quantification of tumor burden versus BLI. We utilized the KCKO murine model of PDAC and subjected tumor-bearing (n = 20) and non-tumor control (NTC) (n = 10) animals to weekly BLI and DEXA measurements for up to 10 weeks. While BLI detected tumors at 1-week, it failed to detect tumor growth, displayed a decreasing trend overtime (slope = -9.0x108; p = 0.0028), and terminal signal did not correlate with ex vivo tumor mass (r = 0.01853; p = 0.6286). In contrast, DEXA did not detect elevated changes in abdominal cavity lean mass until week 2 post inoculation and tumors were not visible until week 3, but successfully quantified a tumor growth trend (slope = 0.7322; p<0.0001), and strongly correlated with final tumor mass (r = 0.9351; p<0.0001). These findings support the use of BLI for initial tumor engraftment and persistence but demonstrate the superiority of DEXA for longitudinal tumor burden studies. As tumor detection by DEXA is not restricted to luciferase expressing models, future studies to assess its value in various cancer models and as an in vivo outcome measure of treatment efficacy are warranted.
Three new species,Xanthomonas hawaiiensissp. nov.,Stenotrophomonas aracearumsp. nov., andStenotrophomonas oahuensissp. nov., isolated from Araceae family
Authors: Chuang Shu-Cheng , Dobhal Shefali , Alvarez Anne M. , Arif Mohammad
Published: September 2023

XanthomonasandStenotrophomonasare closely related genera in the family Lysobacteraceae. In our previous study of aroid-associated bacterial strains, most strains isolated from anthurium, and other aroids were reclassified asX. phaseoliand otherXanthomonasspecies. However, two strains fromSpathiphyllumandColocasiawere phylogenetically distant from other strains in theXanthomonasclade and two anthurium strains clustered within theStenotrophomonasclade. Phylogenetic trees based on 16S rRNA and nine housekeeping genes placed the former strains with type strain ofX. saccharifrom sugarcane and the latter strains with type strain ofS. bentoniticafrom bentonite. In pairwise comparisons with type strains, the overall genomic relatedness indices required delineation of new species; digital DNA-DNA hybridization and average nucleotide identity values were lower than 70% and 95%, respectively. Hence, three new species are proposed:S. aracearumsp. nov. andS. oahuensissp. nov. for two anthurium strains, andX. hawaiiensissp. nov. for the spathiphyllum and colocasia strains. The genome size ofX. hawaiiensissp. nov. is ∼4.88 Mbp and higher thanS. aracearumsp. nov. (4.33 Mbp) andS. oahuensissp. nov. (4.68 Mbp). Pan and core-genome analyses revealed 426 and 576 core genes present in 40 xanthomonads and 25 stenotrophomonads, respectively. The average number of unique genes inStenotrophomonasspp. was higher than inXanthomonasspp. implying higher genetic diversity inStenotrophomonas.