bluuebunny/crossref_metadata_2025 huggingface dataset:
STtools: a comprehensive software pipeline for ultra-high-resolution spatial transcriptomics data
Authors: Xi Jingyue , Lee Jun Hee , Kang Hyun Min , Jun Goo
Published: August 2022

Motivation

While there are many software pipelines for analyzing spatial transcriptomics (ST) data, few can process ultra-high-resolution datasets generated by emerging technologies. There is a clear need for new software tools that can handle submicrometer resolution ST data with computational scalability without compromising its resolution.

Results

We developed STtools, a software pipeline that provides a versatile framework to handle ST datasets with various resolutions, such as the ones produced by Seq-Scope (<1 μm), Slide-seq (10 μm) and VISIUM (100 μm). It automatically processes raw FASTQ files and runs downstream analyses at several folds higher resolution than existing methods. It also generates various visualizations including transcriptome density, cell type mapping, marker gene highlighting and subcellular architectures.

Availability and implementation

STtools is publically available for download at https://github.com/seqscope/STtools

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
The smallest area shaped a big problem: a revision of the placement of the Ventania sky island in the biogeography of South America
Authors: Guerrero Elián L , Apodaca María José
Published: August 2022

The placement of the southern border of the Neotropical region, called the Subtropical Line, is a long-lasting point of discussion. Its most debatable section runs around the Pampean province, where an isolated mountain system called Ventania has Andean connections surrounded by Neotropical biota. To answer where to place the Subtropical Line, a thorough revision of the biogeography of Ventania is needed. Thus, we characterized Ventania as an area of endemism and conducted a similitude analysis to compare it with surrounding systems using stenoic taxa. Then we compiled the disjunct distributions in Ventania and the phylogenetic information of its endemic taxa to know with which other areas it is related. We also compared the biogeographic differences with Tandilia, the nearest mountain system. We found that Ventania is a small but well-defined area of endemism mostly related to the Andean and South American Transition Zone (SATZ) provinces. Relatedness with the Pampean province is less than had been thought. We suggest that Ventania is a SATZ sky island province, and the smallest continental province of the world. The Subtropical Line should therefore be placed in the southern border of the Pampean province, with Ventania as a SATZ island inside the Neotropical region.
A novel cholinergic projection from the lateral parabrachial nucleus and its role in methamphetamine-primed conditioned place preference
Authors: He Teng , Chen Wenwen , Fan Yu , Xu Xing , Guo Hao , Li Nanqin , Lu Xue , Ge Feifei , Guan Xiaowei
Published: August 2022

Drug relapse is a big clinical challenge in the treatment of addiction, but its neural circuit mechanism is far from being fully understood. Here, we identified a novel cholinergic pathway from choline acetyltransferase-positive neurons in the external lateral parabrachial nucleus (eLPBChAT) to the GABAergic neurons in the central nucleus of the amygdala (CeAGABA) and explored its role in methamphetamine priming-induced reinstatement of conditioned place preference. The anatomical structure and functional innervation of the eLPBChAT–CeAGABA pathway were investigated by various methods such as fluorescent micro-optical sectioning tomography, virus-based neural tracing, fibre photometry, patch-clamp and designer receptor exclusively activated by a designer drug. The role of the eLPBChAT–CeAGABA pathway in methamphetamine relapse was assessed using methamphetamine priming-induced reinstatement of conditioned place preference behaviours in male mice. We found that the eLPBChAT neurons mainly projected to the central nucleus of the amygdala. A chemogenetic activation of the eLPBChAT neurons in vitro or in vivo triggered the excitabilities of the CeAGABA neurons, which is at least in part mediated via the cholinergic receptor system. Most importantly, the chemogenetic activation of either the eLPBChAT neurons or the eLPBChAT neurons that project onto the central nucleus of the amygdala decreased the methamphetamine priming-induced reinstatement of conditioned place preference in mice. Our findings revealed a previously undiscovered cholinergic pathway of the eLPBChAT–CeAGABA and showed that the activation of this pathway decreased the methamphetamine priming-induced reinstatement of conditioned place preference.
Public-Interest Litigation before the International Court of Justice: Comment on The Gambia v. Myanmar Case
Authors: Mao Xiao
Published: August 2022

The recent Judgment of the International Court of Justice on the Preliminary Objections in The Gambia v. Myanmar case infers the standing of The Gambia to bring claims before the Court from its “common interest” as a State party to the Genocide Convention. This sweeping approach entails risks of subjectivity and over-breadth. A more nuanced approach, taking into account other features of the treaty in question, should be adopted to determine what obligation would warrant the standing of a State to bring a claim before the Court in respect of its breach. In addition, the adversarial structure of the contentious proceedings of the Court and the procedural rules applicable to it are ill-suited to public-interest litigation, and significant reform of the procedural rules of the Court should be made in order to make public-interest litigation more effective before it.
Phylogenomic Interrogation Revives an Overlooked Hypothesis for the Early Evolution of the Bee Family Apidae (Hymenoptera: Apoidea), With a Focus on the Subfamily Anthophorinae
Authors: Orr Michael C , Branstetter Michael G , Straka Jakub , Yuan Feng , Leijs Remko , Zhang Dan , Zhou Qingsong , Zhu Chao-Dong
Published: August 2022

Despite recent advances in phylogenomics, the early evolution of the largest bee family, Apidae, remains uncertain, hindering efforts to understand the history of Apidae and establish a robust comparative framework. Confirming the position of Anthophorinae—a diverse, globally distributed lineage of apid bees—has been particularly problematic, with the subfamily recovered in various conflicting positions, including as sister to all other Apidae or to the cleptoparasitic Nomadinae. We aimed to resolve relationships in Apidae and Anthophorinae by combining dense taxon sampling, with rigorous phylogenomic analysis of a dataset consisting of ultraconserved elements (UCEs) acquired from multiple sources, including low-coverage genomes. Across a diverse set of analyses, including both concatenation and species tree approaches, and numerous permutations designed to account for systematic biases, Anthophorinae was consistently recovered as the sister group to all remaining Apidae, with Nomadinae sister to (Apinae, [Xylocopinae, Eucerinae]). However, several alternative support metrics (concordance factors, quartet sampling, and gene genealogy interrogation) indicate that this result should be treated with caution. Within Anthophorinae, all genera were recovered as monophyletic, following synonymization of Varthemapistra with Habrophorula. Our results demonstrate the value of dense taxon sampling in bee phylogenomics research and how implementing diverse analytical strategies is important for fully evaluating results at difficult nodes.
A chromosome-level reference genome for the giant pink sea star,Pisaster brevispinus, a species severely impacted by wasting
Authors: DeBiasse Melissa B , Schiebelhut Lauren M , Escalona Merly , Beraut Eric , Fairbairn Colin , Marimuthu Mohan P A , Nguyen Oanh , Sahasrabudhe Ruta , Dawson Michael N
Published: August 2022

Efforts to protect the ecologically and economically significant California Current Ecosystem from global change will greatly benefit from data about patterns of local adaptation and population connectivity. To facilitate that work, we present a reference-quality genome for the giant pink sea star, Pisaster brevispinus, a species of ecological importance along the Pacific west coast of North America that has been heavily impacted by environmental change and disease. We used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly of 550 Mb in length. The assembly contains 127 scaffolds with a contig N50 of 4.6 Mb and a scaffold N50 of 21.4 Mb; the BUSCO completeness score is 98.70%. The P. brevispinus genome assembly is comparable to the genome of the congener species P. ochraceus in size and completeness. Both Pisaster assemblies are consistent with previously published karyotyping results showing sea star genomes are organized into 22 autosomes. The reference genome for P. brevispinus is an important first step toward the goal of producing a comprehensive, population genomics view of ecological and evolutionary processes along the California coast. This resource will help scientists, managers, and policy makers in their task of understanding and protecting critical coastal regions from the impacts of global change.
Countering Commodity Trade Mispricing in Low-Income Countries: A Prescriptive Approach
Authors: Musselli Irene , Bürgi Bonanomi Elisabeth
Published: August 2022

Commodity trade mispricing, especially the undervaluation of commodity exports, disproportionately harms low-income countries that depend on commodity exports for most of their export earnings. Such countries should (re)consider adopting rule-based pricing methods as a prescriptive alternative to transaction-based valuation systems. This article firmly grounds rule-based pricing in market parameters. It calls for a hybrid form of market-based price regulation in the framework of public–private models of supply chain governance, also integrating advice from independent experts. This article addresses this policy option within the parameters set by international law, considering state regulatory scope under international trade and tax law. It challenges the popular objection that prescriptive pricing methods breach international trade and tax rules. Instead, it emphasizes the complexity of any such legal assessment under international economic law.
Reproduction, seasonal morphology, and juvenile growth in three Malagasy fruit bats
Authors: Andrianiaina Angelo , Andry Santino , Gentles Anecia , Guth Sarah , Héraud Jean-Michel , Ranaivoson Hafaliana Christian , Ravelomanantsoa Ny Anjara Fifi , Treuer Timothy , Brook Cara E
Published: August 2022

The island nation of Madagascar is home to three endemic species of Old World fruit bat in the family Pteropodidae: Pteropus rufus, Eidolon dupreanum, and Rousettus madagascariensis, all three of which are IUCN Red Listed under some category of threat. Delineation of seasonal limits in the reproductive calendar for threatened mammals can inform conservation efforts by clarifying parameters used in population viability models, as well as elucidate understanding of the mechanisms underpinning pathogen persistence in host populations. Here, we define the seasonal limits of a staggered annual birth pulse across the three species of endemic Madagascar fruit bat, known reservoirs for viruses of high zoonotic potential. Our field studies indicate that this annual birth pulse takes place in September/October for P. rufus, November for E. dupreanum, and December for R. madagascariensis in central-eastern Madagascar where the bulk of our research was concentrated. Juvenile development periods vary across the three Malagasy pteropodids, resulting in near-synchronous weaning of pups for all species in late January–February at the height of the fruiting season for this region. We here document the size range in morphological traits for the three Malagasy fruit bat species, with P. rufus and E. dupreanum among the larger of pteropodids globally and R. madagascariensis among the smaller. All three species demonstrate subtle sexual dimorphism with males being larger than females. We explore seasonal variation in adult body condition by comparing observed body mass with body mass predicted by forearm length, demonstrating that pregnant females add weight during staggered gestation periods and males lose weight during the nutritionally deficit Malagasy winter. Finally, we quantify forearm, tibia, and ear length growth rates in juvenile bats, demonstrating both faster growth and more protracted development times for P. rufus as compared with E. dupreanum and R. madagascariensis. The longer development period for the already-threatened P. rufus further undermines the conservation status of this species as human hunting is particularly detrimental to population viability during reproductive periods. Our work highlights the importance of longitudinal field studies in collecting critical data for mammalian conservation efforts and human public health alike.
Drivers of a temporal change in the adult sex ratio of a Roosevelt elk (Cervus canadensis roosevelti) population
Authors: Espinoza Zaavian S , Weckerly Floyd W
Published: August 2022

Ecological processes driving female-skewed adult sex ratios (ASRs; males:females) in populations with polygynous mating systems have been addressed theoretically, but empirical support is scarce. The theoretical framework of the female substitution hypothesis (FSH) asserts that a female-skewed ASR at carrying capacity reflects an overall fitness benefit for females and for males competitive in acquiring access to reproductive females. The FSH predicts that as population abundance increases females should acquire forage more efficiently than males, thereby leading to passive displacement of males. The result is declining ASR associated with differential habitat use by both sexes as food resources are depleted by female scramble competition. We characterized the temporal variation in ASR in a Roosevelt elk population inhabiting the Redwood National and State Parks, California, across 24 years, and determined which of two possible ecological mechanisms was the driver of a declining ASR. The first mechanism explored was that increasing female abundance associated with declining forage in the study area led to the passive displacement of males into the study periphery over time. The second mechanism explored was that a declining ASR was precipitated by a lack of males within the study area and the study periphery. Systematic population surveys from a vehicle were done to estimate abundance and ASR as well as assess male abundance in the study periphery. Forage biomass was estimated in quarter-m2 plots randomly placed in meadows inhabited by female elk. Our multiple regression analysis revealed an inverse relationship between abundance and ASR indicating density dependence. We found numerous males in the study periphery when females were abundant. Our least squares models indicated declining food resources across years when female abundance increased. Our results showed that the first, and not the second, ecological mechanism examined was responsible for a female-skewed ASR. Our findings provide empirical support for the theoretical framework of the FSH in a nonmigratory population protected from hunting.
Balamuthia mandrillaris Granulomatous Amoebic Encephalitis: The First African Experience
Authors: Tootla Hafsah D , Eley Brian S , Enslin Johannes M N , Frean John A , Hlela Carol , Kilborn Tracy N , Moodley Bhavani , Peer Shazia , Singh Shivani , Nuttall James J C
Published: August 2022

We report the first case of Balamuthia mandrillaris granulomatous amoebic encephalitis definitively acquired in Africa. Our case emphasizes initial nonspecific dermatological features, delays in confirmation of the diagnosis, difficulties accessing recommended medication, and uncertainty about optimal treatment of a disease with a frequently fatal outcome.
Displaced Selves: Older African Adults in Forced Migration
Authors: Kilpeläinen Faith , Zechner Minna
Published: August 2022

Ageing as a refugee in an unsettled life situation increases the need for identity management due to dramatic life changes. This qualitative study, influenced by phenomenology, focuses on the stories of older adults in protracted intra-African refugee situations and the continuity and discontinuity of their identities. In line with identity process theory, we portray identities as situationally accomplished through the interplay of how one defines oneself internally and how others define one from the outside. The data, analysed by using abductive thematic analysis, consist of five semi-structured interviews with refugees in protracted refugee situations in Nairobi. We argue that older age combined with protracted migratory experiences resulted in the study participants possessing a wide array of experiences, including many losses. These, including their pre-migratory experiences, formed a large repertoire of intra-psychic, interpersonal and intergroup coping strategies to rely on when reworking their identities.
Capsule endoscopy in airway: a difficult extraction
Authors: Tamang Sandeep , Mitnovetski Sergei
Published: August 2022

Foreign bodies of different nature are identified in airway. Extraction of foreign bodies given their dimension and character requires proper set of instruments with right technique to ensure safe removal. Different tools have been discussed to optimally withdraw the object in various articles which have been applied. However, we talk about a case of removal of a pill camera from an elderly patient’s right main bronchus with a certain positioning of the patient after multiple unsuccessful attempts with instruments alone. In conclusion, pill camera as being useful for surveillance for gastrointestinal pathology can have the potential of aspiration.
Spontaneous perforation of pyometra—is hysterectomy required in the emergent setting? A case report and literature review
Authors: Browne Ikennah L
Published: August 2022

Spontaneous perforation of pyometra is a rare event associated with significant morbidity and mortality when diffuse peritonitis is present. While malignant lesions of the cervical tract are the most common cause of pyometra, several benign conditions can contribute to this diagnosis. Traditionally hysterectomy has been the surgical approach of choice for this clinical entity; however, in the setting of septic shock, temporizing techniques may offer the opportunity to stabilize patients and complete a thorough work up before committing to definitive resection. This report explores a case of septic shock secondary to spontaneous perforation of pyometra that was definitively managed with peritoneal lavage and wide drainage. Intraoperative hysteroscopy and uterine biopsy were performed, and no malignancy was identified on final pathology. Intraoperative hysteroscopy along with peritoneal lavage and wide drainage may reduce the morbidity and mortality associated with sepsis from spontaneous perforation of pyometra and potentially avoid unnecessary hysterectomy.
Creation and Internal Validation of a Clinical Predictive Model for Fluconazole Resistance in Patients With Candida Bloodstream Infection
Authors: Rauseo Adriana M , Olsen Margaret A , Stwalley Dustin , Mazi Patrick B , Larson Lindsey , Powderly William G , Spec Andrej
Published: August 2022

Background

Fluconazole is recommended as first-line therapy for candidemia when risk of fluconazole resistance (fluc-R) is low. Lack of methods to estimate resistance risk results in extended use of echinocandins and prolonged hospitalization. This study aimed to develop a clinical predictive model to identify patients at low risk for fluc-R where initial or early step-down fluconazole would be appropriate.

Methods

Retrospective analysis of hospitalized adult patients with positive blood culture for Candida spp from 2013 to 2019. Multivariable logistic regression model was performed to identify factors associated with fluc-R. Stepwise regression was performed on bootstrapped samples to test individual variable stability and estimate confidence intervals (CIs). We used receiver operating characteristic curves to assess performance across the probability spectrum.

Results

We identified 539 adults with candidemia and 72 Candida isolates (13.4%) were fluc-R. Increased risk of fluc-R was associated with older age, prior bacterial bloodstream infection (odds ratio [OR], 2.02 [95% CI, 1.13–3.63]), myelodysplastic syndrome (OR, 3.09 [95% CI, 1.13–8.44]), receipt of azole therapy (OR, 5.42 [95% CI, 2.90–10.1]) within 1 year of index blood culture, and history of bone marrow or stem cell transplant (OR, 2.81 [95% CI, 1.41–5.63]). The model had good discrimination (optimism-corrected c-statistic 0.771), and all of the selected variables were stable. The prediction model had a negative predictive value of 95.7% for the selected sensitivity cutoff of 90.3%.

Conclusions

This model is a potential tool for identifying patients at low risk for fluc-R candidemia to receive first-line or early step-down fluconazole.
Increasing the Demand for Workers with a Criminal Record
Authors: Cullen Zoë , Dobbie Will , Hoffman Mitchell
Published: August 2022

We experimentally test several approaches to increasing the demand for workers with a criminal record on a nationwide staffing platform by addressing potential downside risk and productivity concerns. The staffing platform asked hiring managers to make a series of hypothetical hiring decisions that affected whether workers with a criminal record could accept their jobs in the future. We find that 39% of businesses in our sample are willing to work with individuals with a criminal record at baseline, which rises to over 50% when businesses are offered crime and safety insurance, a single performance review, or a limited background check covering just the past year. Wage subsidies can achieve similar increases but at a substantially higher cost. Based on our findings, the staffing platform relaxed the criminal background check requirement and offered crime and safety insurance to interested businesses.
Is vaccination against COVID-19 associated with autoimmune rheumatic disease flare? A self-controlled case series analysis
Authors: Nakafero Georgina , Grainge Matthew J , Card Tim , Mallen Christian D , Nguyen Van-Tam Jonathan S , Williams Hywel C , Abhishek Abhishek
Published: August 2022

Objectives

To investigate the association between vaccination against coronavirus disease 2019 (COVID-19) and autoimmune rheumatic disease (AIRD) flare.

Material and methods

Patients with AIRDs vaccinated against COVID-19 who consulted for disease flare between 1 December 2020 and 31 December 2021 were ascertained in Clinical Practice Research Datalink (Aurum). AIRD flare was defined as consultation for AIRD with CS prescription on the same day or the next day. Vaccination was defined using date of vaccination and product code. The observation period was partitioned into vaccine-exposed (21 days after vaccination), pre-vaccination (7 days before vaccination) and remaining vaccine-unexposed periods. Participants contributed data with multiple vaccinations and outcomes. Season adjusted incidence rate ratios (aIRR) and 95% CI were calculated using self-controlled case series analysis.

Results

Data for 3554 AIRD cases, 72% female, mean age 65 years and 68.3% with RA, were included. COVID-19 vaccination was associated with significantly fewer AIRD flares in the 21-day vaccine-exposed period when all vaccinations were considered [aIRR (95% CI) 0.89 (0.80, 0.98)]. Using dose-stratified analyses there was a statistically significant negative association in the 21 days after first COVID-19 vaccination but no association after the second or third COVID-19 vaccinations [aIRR (95% CI) 0.76 (0.66, 0.89), 0.94 (0.79, 1.11) and 1.01 (0.85, 1.20), respectively]. On AIRD-type stratified analyses, vaccination was not associated with disease flares. Vaccination without or after severe acute respiratory syndrome coronavirus 2 infection, and with vectored DNA or mRNA vaccines, associated with comparable reduced risk of AIRD flares in the vaccine-exposed period after first COVID-19 vaccination.

Conclusions

Vaccination against COVID-19 was not associated with increased AIRD flares regardless of prior COVID-19, AIRD type, and whether mRNA or DNA vaccination technology were used.
Hate on the Bookshelves: Explaining the Phenomenon of Anti-Korean Hate Books in Japan
Authors: HANSSEN Ulv , WOO Eun Hee
Published: August 2022

Books containing hate speech against Koreans and the Chinese have become a common sight in Japan’s bookshops. The publication of ‘hate books’ has increased in tandem with the struggles of the publishing industry and the deterioration of Japan’s relations with South Korea and China. This article seeks to explain the causes of Japan’s hate book phenomenon, with a particular focus on books targeting Koreans. While South Korean researchers have mainly identified rising nationalism in Japan as the key factor, Japanese analysts label peculiarities in the Japanese publishing industry as the main cause of hate books. We argue that both these explanations are necessary but ultimately insufficient because they ignore each other’s key findings. We propose a synthesized explanation that takes account of both the role of nationalism in creating demand and the unique structure of the Japanese publishing industry, which tends to incentivize the supply of hate books. The article also shows that nationalism only translates into hate book demand in times of diplomatic crisis.
Development and Validation of a High-Throughput Sequencing Test for Mitogenome and rDNA Assembly and Annotation, and Its Use in Support of Nematode Identification of Regulatory Concern
Authors: van de Vossenberg Bart T. L. H. , van Kempen Thijn L. , van Duijnhoven Aron A. L. A. M. , Warbroek Tim , van der Gouw Lucas P. , Apolônio Silva De Oliveira Daniel , van Heese Evelyn Y. J. , Karssen Gerrit
Published: August 2022

Nematoda is a diverse phylum, and representatives are found in most habitats, including in and on animals and plants. Nematodes are regarded as the most abundant group in terms of individuals in marine and terrestrial sediments. Plant-parasitic nematodes are globally responsible for an annual yield loss of $125 billion. Reliable species identification is essential to take appropriate phytosanitary measures. The introduction of validated Sanger sequencing of 18S, 28S, and cox1 barcode loci represented a powerful tool in support of nematode identification. However, technical challenges associated with PCR and Sanger sequencing and the need for additional loci for identification hamper the efficient use of sequence data. To overcome these challenges, we developed an automated bioinformatic pipeline for the assembly and annotation of mitochondrial genomes and ribosomal DNAs, and we defined and validated a standardized test protocol including controls for routine diagnostics (i.e., high-throughput sequencing [HTS] test). The HTS test can be performed on single nematode specimens and outperforms the Sanger-based sequencing by producing less ambiguous consensus sequences and by yielding additional sequence data offering additional diagnostic resolution when needed. Compared with Sanger sequencing, the HTS test represents a reduction in hands-on time. The HTS test is regarded as fit for the purpose of the molecular identification of single nematode specimens in support of nematode diagnostics of regulatory concern.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Endoscopic Treatment of Reflux
Authors: Duarte Chavez Rodrigo , Marino Daniel , Kahaleh Michel , Tyberg Amy
Published: August 2022

The last decade has seen the rise of multiple novel endoscopic techniques to treat gastroesophageal reflux disease, many of which are efficacious when compared with traditional surgical options and allow relief from long-term dependence on antacid medications. This review will explore the latest endoscopic treatment options for gastroesophageal reflux disease including a description of the technique, review of efficacy and safety, and future directions.
Best Practices in Pancreatico-biliary Stenting and EUS-guided Drainage
Authors: Medas Renato , Ferreira-Silva Joel , Girotra Mohit , Barakat Monique , Tabibian James H. , Rodrigues-Pinto Eduardo
Published: August 2022

Indications for endoscopic placement of endoluminal and transluminal stents have greatly expanded over time. Endoscopic stent placement is now a well-established approach for the treatment of benign and malignant biliary and pancreatic diseases (ie, obstructive jaundice, intra-abdominal fluid collections, chronic pancreatitis etc.). Ongoing refinement of technical approaches and development of novel stents is increasing the applicability and success of pancreatico-biliary stenting. In this review, we discuss the important developments in the field of pancreatico-biliary stenting, with a specific focus on endoscopic retrograde cholangiopancreatography and endoscopic ultrasound-associated developments.
Sarcopenia and sarcopenic obesity in chronic kidney disease: update on prevalence, outcomes, risk factors and nutrition treatment
Authors: Barreto Silva Maria Inês , Picard Kelly , Klein Márcia Regina Simas Torres
Published: August 2022

Purpose of review

This review summarizes literature from the last 18 months reporting on sarcopenia (or its components) in chronic kidney disease (CKD).

Recent findings

The prevalence of sarcopenia in CKD is reported to be 5–62.5%, with higher rates observed later in the disease. Sarcopenic obesity rates are reported to be 2–23%. Sarcopenia in CKD is associated with increased risk of mortality, cardiovascular disease and vascular calcification. Risk factors include kidney disease itself and the impacts of CKD on lifestyle (reduced physical activity, diet changes). In earlier stages of CKD, if the risks from sarcopenia outweigh the risk of reaching end-stage renal disease, ensuring adequate energy intake combined with modest protein liberalization and physical activity may be indicated. Protein intakes above 1.3 g/kg of body weight per day should be avoided. For dialysis patients, interventions that provide a combination of carbohydrate, protein and fat appear more effective than those that provide protein alone, though it may take as long as 48 weeks for detectable changes in muscle mass.

Sarcopenia is prevalent in CKD as kidney disease significantly impacts muscle mass and function. Nutrition interventions can improve components of sarcopenia, with an emphasis on adequate energy and protein.
Adenotonsillectomy: the good, the bad and the unknown
Authors: Kaditis Athanasios G. , Gozal David
Published: August 2022

Purpose of review

Adenotonsillar hypertrophy is the most common pathogenetic contributor to obstructive sleep apnea syndrome (OSAS) in childhood, and adenotonsillectomy is the standard initial treatment. Here, we summarize the most recent evidence on the efficacy and complications of adenotonsillectomy and explore knowledge gaps in clinical management.

Recent findings

Favorable adenotonsillectomy effects have been reported in children with very severe OSAS [apnea–hypopnea index (AHI) >20 episodes/h] and extremely severe OSAS (AHI >100 episodes/h), without postoperative mortality, need for endotracheal intubation, prolonged hospital stay or re-admission after hospital discharge. However, the risk of residual OSAS after adenotonsillectomy, which may reach 30–60%, has not been thoroughly established. Behavior, OSAS-related symptoms and quality of life improve postoperatively even in children with AHI 1–5 episodes/h. Natural history of enuresis resolution is accelerated postadenotonsillectomy and office-based systemic blood pressure is decreased in OSAS and hypertension. However, which children younger than 2 years should undergo adenotonsillectomy instead of adenoidectomy only to prevent recurrence of OSAS symptoms and revision surgery remains unclear. Adenotonsillectomy in children with Prader–Willi syndrome is frequently accompanied by postoperative residual OSAS while complications are not uncommon.

In the last 2 years, several studies have provided evidence supporting the efficacy and safety of adenotonsillectomy as treatment intervention for otherwise healthy children with OSAS.
The effect of polymorphisms (M235T and T174M) on the angiotensinogen gene (AGT) in coronary artery disease in the Eastern Asian population: A systematic review and meta-analysis
Authors: Zhang Qian , Huang Qingning , Wang Xianen , Wang Yong , Hua Xiaofang
Published: August 2022

Background:

It is thought that genetic factors may play an important role in the development of coronary artery disease (CAD). Several studies report that AGT polymorphism is implicated in CAD susceptibility, but these results contradict those of the other studies with the associations being unclear in the Eastern Asian population. Therefore, meta-analysis was performed to evaluate this relationship.

Methods:

Publication databases were used to search for eligible relevant studies and valid data were extracted from studies meeting the inclusion criteria. Subsequently, odds ratios (ORs) with 95 % confidence intervals (CIs), were used to assess the strength of the association between AGT polymorphism and CAD risk.

Results:

Seven eligible studies published only in English were included in the present meta-analysis. In the Eastern Asian population, CAD susceptibility was shown to be related to AGT M235T under the heterozygote model (OR = 0.19). Stratified analysis indicated there was a significant relationship between AGT M235T and CAD risk in China under allelic (OR = 1.34), dominant (OR = 1.43), and heterozygote (OR = 1.62) models. The results showed that the T174M polymorphism was significantly associated with CAD risk in recessive (OR = 2.28) and homozygote (OR = 2.37) models in the Eastern Asian population.

Conclusions:

In the Eastern Asian population, especially the Chinese, the M235T of AGT is associated with CAD susceptibility. The T174M polymorphisms were associated with CAD risk in the Eastern Asian population.
Ultrasonic S-Detect mode for the evaluation of thyroid nodules: A meta-analysis
Authors: Bian Jinyi , Wang Ruyue , Lin Mingxin
Published: August 2022

Objectives:

This meta-analysis aimed to evaluate the value of ultrasonic S-Detect mode for the evaluation of thyroid nodules.

Methods:

We searched PubMed, Cochrane Library, and Chinese biomedical databases from inception to August 31, 2021. Meta-analysis was conducted using STATA version 14.0 and Meta-Disc version 1.4 software. We calculated the summary statistics for sensitivity (Sen), specificity (Spe), summary receiver operating characteristic curve, and the area under the curve, and compared the area under the curve between ultrasonic S-Detect mode and thyroid imaging report and data system (TI-RADS) for the diagnosis of thyroid nodules. As a systematic review summarizing the results of previous studies, this study does not need the informed consent of patients or the approval of the ethics review committee.

Results:

Fifteen studies that met all inclusion criteria were included in this meta-analysis. A total of 924 thyroid malignant nodules and 1228 thyroid benign nodules were assessed. All thyroid nodules were histologically confirmed after examination. The pooled Sen and Spe of TI-RADS were 0.89 (95% confidence interval [CI] = 0.85–0.91) and 0.85 (95% CI = 0.78–0.90), respectively; the pooled Sen and Spe of S-Detect were 0.88 (95% CI = 0.85–0.90) and 0.73 (95% CI = 0.63–0.81), respectively. The areas under the summary receiver operating characteristic curve of TI-RADS and S-Detect were 0.9370 (standard error [SE] = 0.0110) and 0.9128 (SE = 0.0147), respectively, between which there was no significant difference (Z = 1.318; SE = 0.0184; P = .1875). We found no evidence of publication bias (t = 0.36, P = .72).

Conclusions:

Our meta-analysis indicates that ultrasonic S-Detect mode may have high diagnostic accuracy and may have certain clinical application value, especially for young doctors.
Long-term prognostic significance of sarcopenia in acute ischemic stroke
Authors: Li Yu-Xuan , Hou Juan , Liu Wen-Ya
Published: August 2022

Because sarcopenia is widely distributed in patients with acute ischemic stroke (AIS) and has not attracted enough attention, this study aims to explore the relationship between sarcopenia defined by temporal muscle thickness (TMT) and physical function and prognosis of patients with AIS. A total of 265 hospitalized nonsurgical AIS patients from 2015 to 2018, with an age range of 28 ~ 92, were analyzed retrospectively. The median value of TMT was used as the risk classification index of sarcopenia. The main results were the relationship between sarcopenia and Essen Stroke Risk Score, National Institutes of Health Stroke Scale, modified Rankin Score, water swallow test, venous thromboembolism assessment of medical inpatients, activities of daily living assessed by Barthel Index, and the relationship between TMT and final survival outcome. The mean TMT of men in the study cohort was higher than that of women. The measured values of TMT among different researchers had good consistency (intraclass correlation coefficient, 0.980; P < .001). After adjusting for confounding variables, logistic regression showed that sarcopenia was associated with Essen Stroke Risk Score (odds ratio, 1.89; P < .05) and Barthel Index (odds ratio, 1.67; P < .05). Kaplan-Meier analysis showed that the survival time of low TMT group was significantly lower than that of high TMT group (36 vs 49 months; P < .001). Multivariate Cox regression showed that there was causal correlation between sarcopenia and patient death (hazard ratio, 3.54; 95% confidence interval, 1.46–8.58; P < .01). As a potential comprehensive index, thickness of temporal muscle can be included in baseline evaluation to show the physical status, stroke recurrence, and survival prognosis of AIS patients.
A narrative review of MRI changes correlated to signs and symptoms of autism
Authors: Faizo Nahla L.
Published: August 2022

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that occurs during early childhood. The change from being normal across several contexts to displaying the behavioral phenotype of ASD occurs in infants and toddlers with autism. Findings provided by magnetic resonance imaging (MRI)-based research owing to the developmental phase, including potential pathways underlying the pathogenesis of the condition and the potential for signs and symptomatic risk prediction. The present study focuses on the characteristic features of magnetic resonance imaging autistic brain, how these changes are correlated to autism signs and symptoms and the implications of MRI as a potential tool for the early diagnosis of ASD.

PRISMA style was used to conduct this review. Research articles related to the key concepts of this review, which is looking at MRI brain changes in autistic patients, were revised and incorporated with what is known with the pathophysiology of brain regions in relation to signs and symptoms of autism.

Studies on brain MRI of autism were revied for major brain features and regions such as brain volume, cortex and hippocampus. This review reveals that brain changes seen in MRI are highly correlated with the signs and symptoms of autism.

There are numerous distinct features noted in an autistic brain using MRI. Based on these findings, various developmental brain paths and autistic behavior culminate in a typical diagnosis, and it is possible that addressing these trajectories would improve the accuracy in which children are detected and provide the necessary treatment.
Neural wedge osteotomy method of correction for cubitus varus deformity in children
Authors: Dai Jin , Zhang Wenyan , Zou Chengda , Yu Gao , Zhao Tantan , Chen Mingchao , Gao Zheming
Published: August 2022

In this study, we evaluated the clinical outcome of neutral wedge osteotomy assisted with the center of rotation of angulation (CORA) method of distal humerus anatomical axis for the treatment of cubitus varus deformity in children. From 2016 to 2019, 20 children with cubitus varus deformity after supracondylar fracture of the humerus were enrolled. Standard anteroposterior radiograph of the humerus was taken preoperatively. The CORA point and angulation angles were obtained by measuring the proximal and distal humerus anatomical axis. During the operation, neutral wedge osteotomy was performed to correct the varus deformity. The Baumann angle and the carrying angle were used to evaluate the correction effect of the distal humeral varus deformity. The average age of the patients was 7.8 years. Patients were followed up for an average of 29.3 months (range, 24–36 months). The average interval between surgery and injury was 12 months. The mean preoperative Baumann angle and carrying angle were 99° (90°–115°) and –14° (range, –10° to –30°), respectively. At the last follow-up, the mean Baumann angle and carrying angle was 76° (70°–80°) and 13.6° (10°–18°), respectively, with 16 cases showing excellent outcome and 4 cases showing good outcome. Our results indicated that the neutral wedge osteotomy assisted with CORA method of distal humerus anatomical axis showed good clinical outcomes in the treatment of cubitus varus deformity in children and is worthy of clinical application. The level of evidence is IV.
Clinical significance of hepatic function in Graves disease with type 2 diabetic mellitus: A single-center retrospective cross-sectional study in Taiwan
Authors: Lee Yi-Wei , Lin Yan-Yu , Weng Shuen-Fu , Hsu Chung-Huei , Huang Chen-Ling , Lin Yu-Pei , Hsieh Yu-Shan
Published: August 2022

Graves disease (GD) and type 2 diabetes mellitus (T2DM) both impair liver function; we therefore explored the possibility of a relationship among diabetic control, thyroid function, and liver function.

This retrospective, cross-sectional study compared serum liver function biomarkers of primary GD patients in a single center between 2016 and 2020, derived from clinical databases, and clarified the correlation of liver function in GD patients with or without T2DM. Furthermore, the diabetes mellitus group was divided into glycated hemoglobin A1C (HbA1C) <6.5% group and ≥6.5% group to further analyze the effect by disease control in patients. Statistical differences between groups were assessed using independent t tests to clarify the association of serum biomarkers between GD with T2DM. Pearson test was applied to assess within-group statistical correlation of serum biomarkers. The correlation of factors in each group was demonstrated by using the Kendall tau-b method and stepwise regression analysis.

A total of 77 patients were included in the study. In the study population, glutamate pyruvate transaminase (GPT) was significantly correlated with thyroid-stimulating hormone, and HbA1C was significantly correlated with alkaline phosphatase (ALK-P), glutamate oxaloacetate transaminase (GOT), and GPT. An examination of GOT, GPT, free thyroxine (FT4), and HbA1C levels revealed a significant difference between the non-T2DM and T2DM groups. GPT also exhibited a significant correlation with triiodothyronine in the T2DM group. The T2DM group was further divided into groups: HbA1C <6.5% and ≥6.5%. The results demonstrated that ALK-P, GOT, GPT, and FT4 levels were significantly different between the groups. A significant correlation between ALK-P and thyroid-stimulating hormone and between GOT and FT4 was also identified in the HbA1C <6.5% group.

Our single-center study revealed that diabetes affects liver function in patients with GD. For patients with T2DM, when liver function becomes impaired, thyroid function control deteriorates. GPT was correlated with triiodothyronine but not with FT4, which indicated the impairment of deiodination in the liver. This phenomenon was not observed in the non-T2DM population. The early detection of abnormal liver function in patients with GD and T2DM may help limit the development of comorbidities and improve disease management.
Solid pseudopapillary neoplasms of the pancreas: Is there a factor determining the prognosis? Experience of a single institution
Authors: Tasar Pinar , Kilicturgay Sadik Ayhan
Published: August 2022

Solid pseudopapillary neoplasms (SPNs) are frequently seen in young women. Although the behavior pattern varies, these rare lesions generally have a low malignant potential. In this study, the aim was to investigate the effect of clinicopathological features of lesions on the recurrence in and survival of patients. In this study, patients of our clinic who were pathologically diagnosed with SPN after pancreatic surgery between July 2008 and December 2020 were evaluated retrospectively. Patients’ age, gender, comorbidities, symptoms at the time of application, preoperative CA 19-9, CEA value, preoperative cross-sectional diagnostic imaging method and lesion characteristics, surgery, postoperative complications, length of hospital stay, and histopathological features were evaluated. Early and late mortality, overall survival, disease-free survival, and recurrence rate were determined. Four of the 23 patients diagnosed with SPN were male and the median age was 29 (23–47) years. Of the study patients, 69.56% experienced pain symptoms and 30.43% were asymptomatic. The median tumor size was 4 cm (1.5–15). The most common surgical procedure was distal pancreatectomy (56.5%). The median length of hospital stays was 5 (3–120) days and morbidity was observed in 9 cases (39.13%). The mortality rate was 4.35%. The mean follow-up period in the series was 53 (8–132) months and none of the patients developed recurrence. In this study, no significant difference was found regarding recurrence in patients with SPN with histopathologically aggressive biological behavior. The overall survival rate was 95.7%. SPNs are rare lesions with low malignant potential. SPNs are associated with longer-term survival after surgical resection.
Diagnostic utility of clinical characteristics, laboratory tests, and serum ferritin in diagnosis of adult-onset Still disease
Authors: Sagy Iftach , Finkel-Oron Alona , Naamany Eviatar , Barski Leonid , Abu-Shakra Mahmoud , Molad Yair , Shiber Shachaf
Published: August 2022

The diagnosis of adult-onset Still disease (AOSD) is challenging with ambiguous clinical presentation and no specific serological markers. We aim to evaluate the diagnostic utility of clinical, laboratory and serum ferritin features in established AOSD patients. We included all patients >18 years who were admitted to 2 tertiary medical centers (2003–2019) with serum ferritin above 1000 ng/mL. AOSD patients and non-AOSD controls were matched in 1:4 ratio for age and sex. The primary outcomes were sensitivity, specificity, positive/negative likelihood ratio and area under the curve (AUC) using clinical and laboratory characteristics based on the Yamaguchi classification criteria, in addition to serum ferritin. We identified 2658 patients with serum ferritin above 1000 ng/m, of whom 36 diagnosed with AOSD and 144 non-AOSD matched controls. Presence of arthralgia/arthritis showed the highest sensitivity (0.74), specificity (0.93), positive likelihood ratio (10.69), negative likelihood ratio (0.27) and AUC (0.83, 95% confidence interval 0.74–0.92) to the diagnosis of AOSD. On the other hand, serum ferritin showed variation and poorer results, depends on the chosen ferritin cutoff. Joint involvement showed the best diagnostic utility to establish the diagnosis of AOSD. Although clinicians use often elevated ferritin levels as an anchor to AOSD, the final diagnosis should be based on thorough clinical evaluation.