bluuebunny/crossref_metadata_2025 huggingface dataset:
FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations
Authors: Zhou Nan , Yuan Xiaoqing , Du Qingsong , Zhang Zhiyu , Shi Xiaolei , Bao Jinku , Ning Yuping , Peng Li
Published: October 2022

Ferroptosis is a mode of regulated cell death characterized by iron-dependent accumulation of lipid peroxidation. It is closely linked to the pathophysiological processes in many diseases. Since our publication of the first ferroptosis database in 2020 (FerrDb V1), many new findings have been published. To keep up with the rapid progress in ferroptosis research and to provide timely and high-quality data, here we present the successor, FerrDb V2. It contains 1001 ferroptosis regulators and 143 ferroptosis-disease associations manually curated from 3288 articles. Specifically, there are 621 gene regulators, of which 264 are drivers, 238 are suppressors, 9 are markers, and 110 are unclassified genes; and there are 380 substance regulators, with 201 inducers and 179 inhibitors. Compared to FerrDb V1, curated articles increase by >300%, ferroptosis regulators increase by 175%, and ferroptosis-disease associations increase by 50.5%. Circular RNA and pseudogene are novel regulators in FerrDb V2, and the percentage of non-coding RNA increases from 7.3% to 13.6%. External gene-related data were integrated, enabling thought-provoking and gene-oriented analysis in FerrDb V2. In conclusion, FerrDb V2 will help to acquire deeper insights into ferroptosis. FerrDb V2 is freely accessible at http://www.zhounan.org/ferrdb/.
RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures
Authors: Kushner Artem , Petrov Anton S , Dao Duc Khanh
Published: October 2022

Recent advances in Cryo-EM led to a surge of ribosome structures deposited over the past years, including structures from different species, conformational states, or bound with different ligands. Yet, multiple conflicts of nomenclature make the identification and comparison of structures and ortholog components challenging. We present RiboXYZ (available at https://ribosome.xyz), a database that provides organized access to ribosome structures, with several tools for visualisation and study. The database is up-to-date with the Protein Data Bank (PDB) but provides a standardized nomenclature that allows for searching and comparing ribosomal components (proteins, RNA, ligands) across all the available structures. In addition to structured and simplified access to the data, the application has several specialized visualization tools, including the identification and prediction of ligand binding sites, and 3D superimposition of ribosomal components. Overall, RiboXYZ provides a useful toolkit that complements the PDB database, by implementing the current conventions and providing a set of auxiliary tools that have been developed explicitly for analyzing ribosome structures. This toolkit can be easily accessed by both experts and non-experts in structural biology so that they can search, visualize and compare structures, with various potential applications in molecular biology, evolution, and biochemistry.
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes
Authors: Dong Mei-Jing , Luo Hao , Gao Feng
Published: October 2022

DoriC was first launched in 2007 as a database of replication origins (oriCs) in bacterial genomes and has since been constantly updated to integrate the latest research progress in this field. The database was subsequently extended to include the oriCs in archaeal genomes as well as those in plasmids. This latest release, DoriC 12.0, includes the oriCs in both draft and complete prokaryotic genomes. At the same time, the number of oriCs in the database has also increased significantly and currently contains over 200 000 bacterial entries distributed in more than 40 phyla. Among them, a large number are from bacteria in new phyla whose oriCs were not explored before. Additionally, new oriC features and improvements have been introduced, especially in the visualization and analysis of oriCs. Currently, DoriC is considered as an important database in the fields of bioinformatics, microbial genomics, and even synthetic biology, providing a valuable resource as well as a comprehensive platform for the research on oriCs. DoriC 12.0 can be accessed at https://tubic.org/doric/ and http://tubic.tju.edu.cn/doric/.
Habit formation and trade unions
Authors: Goerke Laszlo , Hartmann Sven A
Published: October 2022

We analyse how habit formation affects collective bargaining outcomes if a firm-specific trade union determines wages. For a wide variety of alternative analytical settings, such internal reference points induce the union to increase wages over time. A numerical example suggests that the resulting decline in employment can be substantial. Furthermore, policy changes in one period, which are either reversed in the next or anticipated in previous periods, have effects on wage outcomes for multiple periods because they affect the habit stock at times at which they are not yet or no longer in operation.
Liver Disease and Treatment Needs of Asymptomatic Persons Living With Hepatitis B in Senegal
Authors: Ramírez Mena Adrià , Thioubou Mame Aissé , Diallo Kalilou , Tine Judicaël , Ngom Ndeye Fatou , Fortes Louise , Ndiaye Kiné , Karasi Jean-Claude , Seguin-Devaux Carole , Goedertz Henri , Diouf Daouda , Seydi Moussa , Sambou Benjamin Amaye , Arendt Vic , Wandeler Gilles , Manga Noël Magloire ,   for SEN-B and CARES
Published: October 2022

The prevalence of active hepatitis B among asymptomatic persons remains unclear in Africa. Of 1206 newly diagnosed persons in Senegal, 12.3% had significant fibrosis and 31.3% had hepatitis B virus (HBV) DNA levels >2000 IU/mL. Overall, 128 (12.9%) were eligible for antiviral therapy. Generalized HBV screening allowed the identification of a large population requiring HBV care.
Patient Outcomes from Multidisciplinary Chronic Pain Programs in Safety Net Clinics: A Scoping Review
Authors: Sheffield Bernadette , Lewis Kelsey , Battaglia Patrick
Published: October 2022

Patients within the safety net, defined as gap healthcare services for un- or under-insured persons, disproportionately suffer high impact chronic pain. The purpose of this review was to examine pain-related outcomes from multidisciplinary programs for patients with chronic pain within the safety net. A scoping review was conducted based on the Arksey and O’Malley framework coupled with the Preferred Reporting Items for Systematic reviews and Meta-Analyses-Scoping Review checklist. CINAHL, MEDLINE, PubMed, and Google Scholar were searched for eligible articles published between January 1, 2010, and December 31, 2020. Grey literature was searched by typing relevant keywords into Google. Quantitative and qualitative outcomes were included. Data collected were charted and analyzed. Ten articles were included, with five demonstrating primarily quantitative results, three demonstrating primarily qualitative results, and the remaining two demonstrating primarily mixed results. Of the studies that utilized qualitative measures, themes included reduction in pain symptoms and the positive reception of a group-based pain management approach. Of the studies that employed quantitative measures, most demonstrated improvements in pain-related outcomes post-intervention, although not all statistically significant. Multidisciplinary pain programs may be of benefit to safety net patients with chronic pain. Further data collection is needed to determine the efficacy of these programs.
Trendy Business Cycles and Asset Prices
Authors: Davis Jesse , Segal Gill
Published: October 2022

The data-generating process underlying productivity includes both trend and business cycle shocks, generating counterfactuals for prices under full information. In practice, agents’ inability to immediately distinguish between the two shocks creates “rational confusion”: each shock inherits properties of its counterpart. This confusion magnifies the perceived share of permanent shocks and implies that, contrary to canonical frameworks, transitory shocks are the main driver of long-run risk through trendy business cycles. With learning, the equity premium turns positive, while investment and valuation ratios become procyclical, as in the data. Consequently, rational confusion is key for reconciling disciplined macro-dynamics with equilibrium

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Semantic and Acoustic Markers in Schizophrenia-Spectrum Disorders: A Combinatory Machine Learning Approach
Authors: Voppel Alban E , de Boer Janna N , Brederoo Sanne G , Schnack Hugo G , Sommer Iris E C
Published: October 2022

Background and hypothesis

Speech is a promising marker to aid diagnosis of schizophrenia-spectrum disorders, as it reflects symptoms like thought disorder and negative symptoms. Previous approaches made use of different domains of speech for diagnostic classification, including features like coherence (semantic) and form (acoustic). However, an examination of the added value of each domain when combined is lacking as of yet. Here, we investigate the acoustic and semantic domains separately and combined.

Study design

Using semi-structured interviews, speech of 94 subjects with schizophrenia-spectrum disorders (SSD) and 73 healthy controls (HC) was recorded. Acoustic features were extracted using a standardized feature-set, and transcribed interviews were used to calculate semantic word similarity using word2vec. Random forest classifiers were trained for each domain. A third classifier was used to combine features from both domains; 10-fold cross-validation was used for each model.

Results

The acoustic random forest classifier achieved 81% accuracy classifying SSD and HC, while the semantic domain classifier reached an accuracy of 80%. Joining features from the two domains, the combined classifier reached 85% accuracy, significantly improving on separate domain classifiers. For the combined classifier, top features were fragmented speech from the acoustic domain and variance of similarity from the semantic domain.

Conclusions

Both semantic and acoustic analyses of speech achieved ~80% accuracy in classifying SSD from HC. We replicate earlier findings per domain, additionally showing that combining these features significantly improves classification performance. Feature importance and accuracy in combined classification indicate that the domains measure different, complementing aspects of speech.
Psychotic Disorders in Adolescence and Later Long-term Exclusion From Education and Employment
Authors: Ringbom Ida , Suvisaari Jaana , Kääriälä Antti , Sourander Andre , Gissler Mika , Kelleher Ian , Gyllenberg David
Published: October 2022

Background and hypothesis

Psychotic disorders have been associated with not being in education, employment, and training (NEET). There is a lack of knowledge on the importance of risk markers for NEET among people with psychotic disorders and what rehabilitation they receive.

Study design

We based our research on the register-based 1987 Finnish Birth Cohort study, which included all live births in Finland during that year. The study cohort were 288 people who had been diagnosed with psychotic disorders during 2004–2007, when they were 16–20 year old, and 55 883 who had not. We looked at the national register data for those subjects in 2008–2015, when they were 20–28 year old, and compared any associations between sociodemographic factors and NEET status.

Study results

NEET for more than 5 year affected 2.2% of those without psychosis, 35.8% of those with any nonaffective psychotic disorder, and 57.0% of those with schizophrenia or schizoaffective disorders. Family-related risk factors were weaker predictors of long-term NEET in subjects with psychotic disorders than other cohort members. Having a psychotic disorder plus long-term NEET was associated with not applying for upper secondary education, not finishing upper secondary education, parents receiving welfare benefits, being diagnosed with schizophrenia or schizoaffective disorders and being hospitalized for psychosis. Only 24.3% with psychotic disorders had participated in vocational rehabilitation.

Conclusions

A diagnosis of psychosis in adolescence is independently associated with serious long term functional disability. Among those with psychotic disorders, educational problems are markers for adverse labor market outcomes. Despite this, vocational rehabilitation is seldom provided.
Language Network Dysfunction and Formal Thought Disorder in Schizophrenia
Authors: Palaniyappan Lena , Homan Philipp , Alonso-Sanchez Maria F
Published: October 2022

Background

Pathophysiological inquiries into schizophrenia require a consideration of one of its most defining features: disorganization and impoverishment in verbal behavior. This feature, often captured using the term Formal Thought Disorder (FTD), still remains to be one of the most poorly understood and understudied dimensions of schizophrenia. In particular, the large-scale network level dysfunction that contributes to FTD remains obscure to date.

Study Design

In this narrative review, we consider the various challenges that need to be addressed for us to move towards mapping FTD (construct) to a brain network level account (circuit).

Study Results

The construct-to-circuit mapping goal is now becoming more plausible than it ever was, given the parallel advent of brain stimulation and the tools providing objective readouts of human speech. Notwithstanding this, several challenges remain to be overcome before we can decisively map the neural basis of FTD. We highlight the need for phenotype refinement, robust experimental designs, informed analytical choices, and present plausible targets in and beyond the Language Network for brain stimulation studies in FTD.

Conclusions

Developing a therapeutically beneficial pathophysiological model of FTD is a challenging endeavor, but holds the promise of improving interpersonal communication and reducing social disability in schizophrenia. Addressing the issues raised in this review will be a decisive step in this direction.
Hidden diversity of the genus Trinomys (Rodentia: Echimyidae): phylogenetic and populational structure analyses uncover putative new lineages
Authors: Nacif Camila Leitão , Bastos Diogo Lisbôa , Mello Beatriz , Lazar Ana , Hingst-Zaher Erika , Geise Lena , Bonvicino Cibele Rodrigues
Published: October 2022

Trinomys, one of the most species-rich spiny rat genera in Brazil, is widely distributed in Caatinga, Cerrado and Atlantic Forest biomes, and currently includes ten recognized species, three of which are polytypic. Although some studies employing molecular data have been conducted to better characterize phylogenetic relationships among species, 19 nominal taxa have been suggested, implying considerable incongruence regarding species boundaries. We addressed this incongruence by intensively sampling all species across the geographic distribution of the genus. In addition to publicly available data, we generated 182 mt-Cytb gene sequences, and employed phylogenetic and computational species delimitation methods to obtain a clearer picture of the genus diversity. Moreover, we evaluated populational diversity within each accepted species, considering their geographical distribution and a timescale for the evolution of the genus. Beyond confirming the general patterns described for the evolution of the group, this new analysis suggests that Trinomys is comprised of at least 16 evolutionary lineages, 13 of them recognized as species or subspecies, and three never before characterized. This study highlights the importance of increased sample sizes and computational species delimitation methods in uncovering hidden diversity in Trinomys.
Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study
Authors: Pinho Catarina , Kaliontzopoulou Antigoni , Ferreira Carlos A , Gama João
Published: October 2022

Automated image classification is a thriving field of machine learning, and various successful applications dealing with biological images have recently emerged. In this work, we address the ability of these methods to identify species that are difficult to tell apart by humans due to their morphological similarity. We focus on distinguishing species of wall lizards, namely those belonging to the Podarcis hispanicus species complex, which constitutes a well-known example of cryptic morphological variation. We address two classification experiments: (1) assignment of images of the morphologically relatively distinct P. bocagei and P. lusitanicus; and (2) distinction between the overall more cryptic nine taxa that compose this complex. We used four datasets (two image perspectives and individuals of the two sexes) and three deep-learning models to address each problem. Our results suggest a high ability of the models to identify the correct species, especially when combining predictions from different perspectives and models (accuracy of 95.9% and 97.1% for females and males, respectively, in the two-class case; and of 91.2% to 93.5% for females and males, respectively, in the nine-class case). Overall, these results establish deep-learning models as an important tool for field identification and monitoring of cryptic species complexes, alleviating the burden of expert or genetic identification.
Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer
Authors: Kronmiller Brent A. , Feau Nicolas , Shen Danyu , Tabima Javier F. , Ali Shahin S. , Armitage Andrew D. , Arredondo Felipe , Bailey Bryan A. , Bollmann Stephanie R. , Dale Angela , Harrison Richard J. , Hrywkiw Kelly , Kasuga Takao , McDougal Rebecca , Nellist Charlotte F. , Panda Preeti , Tripathy Sucheta , Williams Nari M. , Ye Wenwu , Wang Yuanchao , Hamelin Richard C. , Grünwald Niklaus J.
Published: October 2022

Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual Phytophthora species and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, and plant host range. Predicted numbers of apoplastic effectors increased as the host range of Phytophthora species increased. Predicted numbers of cytoplasmic effectors also increased with host range but leveled off or decreased in Phytophthora species that have enormous host ranges. With extensive sequencing across the Phytophthora genus, we now have the genomic resources to evaluate horizontal gene transfer events across the oomycetes. Using a machine-learning approach to identify horizontally transferred genes with bacterial or fungal origin, we identified 44 candidates over 36 Phytophthora species genomes. Phylogenetic reconstruction indicates that the transfers of most of these 44 candidates happened in parallel to major advances in the evolution of the oomycetes and Phytophthora spp. We conclude that the 31 genomes presented here are essential for investigating genus-wide genomic associations in genus Phytophthora.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Identification and Genome-Wide Association Analysis for Fusarium Crown Rot Resistance in Wheat
Authors: Lin Yu , Chen Hao , Yan Ning , Li Chao , Hou Shuai , Mou Yuzhou , Wu Fangkun , Wang Zhiqiang , Shi Haoran , Li Caixia , Liu Yaxi
Published: October 2022

Fusarium crown rot (FCR) is a fungal disease and severely decreases wheat production worldwide. Tibetan semiwild wheat, Yunnan hulled wheat, Xinjiang rice wheat, and Sichuan white wheat are four subspecies landraces endemic to western China and have rich genetic diversity in response to biotic and abiotic stresses. Here, a natural population, including 209 wheat accessions of four subspecies, was evaluated for FCR resistance. he genome-wide association study was performed using the wheat 55K single-nucleotide polymorphisms (SNPs). The results showed that the disease index (DI) ranged from 16.88 to 85.00, while six accessions showed moderate to high resistance (DI ≤ 30). Genome-wide association analysis identified 10 stable loci for FCR resistance on chromosomes 1B, 2A (5), 5A, 7A, 7B, and 7D. Four major loci—Qfcr.sicau.2A-1, Qfcr.sicau.2A-3, Qfcr.sicau.5A, and Qfcr.sicau.7D—explained 6.01 to 14.48, 9.76 to 13.11, 8.19 to 10.29, and 5.76 to 12.21% phenotypic variation, respectively. Quantitative trait loci (QTL) pyramiding analysis of these four major loci revealed that accessions with four resistance haplotypes could significantly decrease FCR severity by 9.35 to 31.61% compared with those without or with one to three resistance haplotypes. One kompetitive allele-specific PCR (KASP) marker each was successfully developed for Qfcr.sicau.2A-1 and Qfcr.sicau.7D. The KASP marker of Qfcr.sicau.2A-1 was used to genotype in an F6 recombinant inbred line population. The result showed that the lines carrying the resistance allele reduced FCR severity by 17.78%, demonstrating the importance of Qfcr.sicau.2A-1 in resistance breeding programs. Our findings provide valuable QTL and breeder-friendly PCR-based markers for applications in FCR resistance breeding programs. Our study also proved that gene pyramiding of major loci could enhance FCR resistance.
PTEN‐knockout regulates metabolic rewiring and epigenetic reprogramming in prostate cancer and chemoprevention by triterpenoid ursolic acid
Authors: Wang Lujing , Wang Chao , Sarwar Md. Shahid , Chou Pochung , Wang Yujue , Su Xiaoyang , Kong Ah‐Ng Tony
Published: October 2022

PTEN (phosphatase and tensin homolog deleted on chromosome 10) is one of the most frequently mutated/deleted tumor suppressor genes in many human cancers. Ursolic acid (UA) is a natural triterpenoid possessing antioxidant, anti‐inflammatory, and anticancer effects. However, how PTEN impacts metabolic rewiring and how UA modifies PTEN‐driven metabolic and epigenetic reprogramming in prostate cancer (PCa) remains unknown. In the current study, we found that UA protects against PTEN knockout (KO)‐induced tumorigenesis at different stages of PCa. Epigenomic CpG methyl‐seq revealed UA attenuated PTEN KO‐induced differentially methylated regions (DMRs) profiles. Transcriptomic RNA‐seq showed UA abrogated PTEN KO‐induced differentially expressed genes (DEGs) of PCa‐related oncogenes' Has3, Cfh, and Msx1 overexpression, indicating UA plays a crucial role in PTEN KO‐mediated gene regulation and its potential consequences on cancer interception. Association analysis of DEGs and DMRs identified that the mRNA expression of tumor suppressor gene BDH2, and oncogenes Ephas, Isg15, and Nos2 were correlated with the promoter CpG methylation status in the early‐stage comparison groups indicating UA could regulate the oncogenes or tumor suppressor genes by modulating their promoter methylation at an early stage of prostate tumorigenesis. The metabolomic study showed UA attenuated PTEN KO‐regulated cancer‐associated metabolisms like purine metabolism/metabolites correlating with RNAseq findings, glycolysis/gluconeogenesis metabolism, as well as epigenetic‐related metabolites pyruvate and lactate indicating UA plays a critical role in PTEN KO‐mediated metabolic and epigenetic reprogramming and its consequences on cancer development. In this context, UA impacts metabolic rewiring causing epigenetic and transcriptomic reprogramming potentially contributing to the overall protection against prostate‐specific PTEN KO‐mediated PCa.
Is immunotherapy safe for treatment of severe asthma
Authors: Epstein Tolly E.G. , Calabria Christopher W.
Published: October 2022

Purpose of review

The benefits of allergen immunotherapy (AIT), including subcutaneous allergen immunotherapy (SCIT) and sublingual allergen immunotherapy (SLIT), for IgE-mediated asthma are well established, especially for dust mite. This review will explore whether the benefits of AIT outweigh the risks in severe asthmatic patients.

Recent findings

Studies have mostly included mild and moderate asthmatic patients, but at least a few studies do show improvements in asthma symptoms and medication use in severe asthmatic patients. Asthma, and especially uncontrolled asthma, is a major risk factor for severe and fatal systemic reactions from SCIT. Uncontrolled asthma is an absolute contraindication for SCIT. It is less clear whether the benefits of SCIT and SLIT may outweigh the risks in well controlled, severe asthmatic patients, and further study is needed in this area. Asthma biologics, especially Omalizumab, may improve outcomes in severe, controlled asthmatic patients on SCIT, but further data are needed regarding timing of initiation and duration of treatment.

Although severe asthmatic patients may benefit from AIT, significant risks exist, especially in those with uncontrolled asthma. Further study is needed regarding optimal strategies to minimize risks.
Butyrate ameliorates colorectal cancer through regulating intestinal microecological disorders
Authors: Kang Jingjing , Sun Mingzhong , Chang Yi , Chen Hongmei , Zhang Juan , Liang Xiaodong , Xiao Tengfei
Published: October 2022

The occurrence and progression of colorectal cancer (CRC) are closely related to intestinal microecological disorders. Butyrate, the representative of short chain fatty acids, possess anti-inflammatory and antioxidant effects, and its antitumor effect has been gradually paid attention to. In this study, azoxymethane/dextran sodium sulfate induced mouse CRC model was used to explore the role and mechanism of butyrate in regulating colon cancer and its intestinal microecological balance. Outcomes exhibited that butyrate alleviated weight loss, disease activity index, and survival in CRC mice and inhibited tumor number and progression. Further research revealed that butyrate restrained the aggregation of harmful while promoting the colonization of beneficial flora, such as Actinobacteriota, Bifidobacteriales and Muribaculacea through 16S rDNA sequence analysis. This study confirmed that butyrate can ameliorate CRC by repairing intestinal microecology, providing ideas and evidence for chemical prophylactic agents, such as butyrate to remedy tumors and regulate tumor microbiota.
Plastic Surgery in the Gulf Cooperation Council Countries: Role of Telemedicine
Authors: Amir Mrad Mohamed , Kattan Abdullah E. , Al Fardan Zuhair , Alhumsi Taghreed R. , Al Saud Nouf A. , Alshomer Feras M. , Alanazi Shahad N. , Shah Mardan Qutaiba N.M.
Published: October 2022

Background:

Internationally, telemedicine is finding its way into common day plastic surgery practice as a result of the COVID-19 pandemic. Nonetheless, no data about its practice in the Gulf region are available to date.

Methodology:

This is a cross-sectional survey-based study that was sent online to the plastic surgeons practicing in the Gulf region. The study aimed to look into the integration of telemedicine into the practice and the surgeons’ attitude and future vision about it. Participation was voluntary, and confidentiality was preserved.

Results:

A total of 229 plastic surgeons enrolled in this study in mid-2020. There were 192 male participants (83.8%) and 37 female participants (16.2%). Of these, 99 (43.2%) practiced in Saudi Arabia, 85 (37.1%) in the United Arab Emirates, 24 (10.5%) in Oman, 18 (7.9%) in Kuwait, and three (1.3%) in Bahrain. In total, 85 (37.1%) used telemedicine during lockdown, and 144 (62.9%) thought that its usage will remain beneficial in the future. There was no significant difference in practicing telemedicine in different plastic surgery subspecialties, varying level of experience, and country of practice. Among those who used virtual consultations, 62 (72.9%) did not charge for consultation fees.

Conclusion:

The tendency toward telemedicine integration in plastic surgery practice is growing worldwide, especially after COVID-19. Its limitations are outweighed by its advantages and, with time, many of these will be bypassed. New innovations driven by advancement in technology will further embed telemedicine into the practice.
The dynamics of integration and integrated care
Authors: Clark Jonathan R. , Tietschert Maike , Kerrissey Michaela , Friedberg Mark , Singer Sara J.
Published: October 2022

Background

Substantial variation exists in how well health care is integrated, even across similarly structured organizations, yet research about what physician organizations (POs) do that enables or inhibits integrated care is limited.

Purpose

The aim of this study was to explore the dynamics that enable POs to integrate care.

Methodology/Approach

We ranked a stratified sample of POs according to patient perceptions of integrated care, as measured in a survey. We interviewed professionals, patients, and family members in 10 higher and 3 lower ranked POs about the process of caring for patients with complex conditions. We derived integration-related themes from the interview data and quantified their prevalence. Using a quasi-statistical approach, we explored relationships among themes and their associations with patient perceptions of integrated care.

Results

From 6,104 coded references, we derived a set of themes representing integration perspectives, integration engagement mechanisms, and integration failures. POs experienced frequent integration failures. Higher ranked POs experienced these failures less often because of a combination of functional, interpersonal, and stakeholder engagement mechanisms, which appear to complement one another. Integration perspectives, including both people-oriented and systems-oriented mindsets, appear to play a role in generating these integration dynamics.

Conclusion

Delivering integrated care depends on a PO’s ability to limit integration failures, keeping provider attention focused on patients. Building on the attention-based view, we present a framework suggesting that this ability is a function of both integration perspectives and integration engagement mechanisms.

Practice Implications

POs interested in delivering more integrated care should employ a variety of complementary integration engagement mechanisms and facilitate these efforts by nurturing both people-oriented and system-oriented mindsets among PO decision-makers.
Management of inflammation after the cataract surgery
Authors: Grzybowski Andrzej , Sidaraite Agne , Zemaitiene Reda
Published: October 2022

Purpose of review

To review most recent studies and clinical trials regarding pathogenesis, treatment, and prevention of inflammation after the cataract surgery.

Recent findings

FLACS gave opportunity to evaluate inflammatory cytokines in the aqueous humour right after the laser procedure, which led to acknowledging the inflammation pathogenesis during the phacoemulsification. Although there is still a lack of evidence, which would prove the long-term benefit of NSAIDs, they are indicated and effective when risk factors for PCME are present. PREMED studies showed that combination of NSAID and steroids after the surgery for healthy subjects is cost-effective. The triamcinolone injection together with topical steroids and NSAIDs for diabetic patients after the cataract surgery was the most cost-effective in preventing PCME according to the PREMED. Dropless cataract surgery is another emerging topic: dexamethasone implants and suspensions look promising as we await more clinical trials with drug-loaded IOLs.

Inflammation after the cataract surgery can be prevented, and these methods are one of the most essential topics with growing phacoemulsification rate. Topical NSAIDs are cost-effective not only for patients with risk factors for PCME but also for healthy subjects. New dropless techniques are being successfully introduced in the clinical practice.
Providing a Constipation Action Plan to Families of Children With Constipation Decreases Health Care Utilization
Authors: Hawa Kathryn , Janse Sarah , Lee Jennifer , Bali Neetu , Vaz Karla , Yacob Desale , Di Lorenzo Carlo , Lu Peter L.
Published: October 2022

Objectives:

To evaluate whether providing a constipation action plan (CAP) to families of children with constipation at outpatient gastroenterology (GI) visits affects health care utilization of the GI department.

Methods:

We created a CAP to be included in the after visit summary of children seen in our GI Clinic. We compared the number of patient telephone calls, electronic messages, and urgent care (UC) visits, emergency department (ED) visits, and hospitalizations within 3 months after the visit of patients who received the CAP compared to those who did not using inverse probability treatment weighting (IPTW) analysis. For families who received the CAP at a follow‐up visit, we compared these variables in the 3 months before and after the CAP was provided using paired t test and McNemar’s test as appropriate.

Results:

We included 336 patients who received the CAP and 2812 who did not. After IPTW adjustment, there were fewer patient telephone calls for patients who received the CAP (P = 0.0006). The difference in patient electronic messages was not statistically significant (P = 0.09). For the 45 patients who received the CAP at a follow‐up visit, there were on average 1.8 more patient telephone calls made prior to receiving the CAP than after (95% confidence interval (CI) = 0.8–2.8; P = 0.0007) and 2.3 more patient electronic messages received (95% CI = 0.1–4.5; P = 0.04). There were no differences in UC/emergency department visits or hospitalizations.

Conclusions:

We found that providing a CAP to families of children with constipation decreases health care utilization. Further studies are needed to determine whether this impacts patient outcomes.
Pre‐endoscopy Symptoms and Age, But Not Esophageal Biopsy Number Are Associated With Post‐endoscopy Adverse Events
Authors: Wenzel Amanda A. , Kagalwalla Amir F. , Wechsler Joshua B.
Published: October 2022

Esophagogastroduodenoscopy (EGD) is a frequently utilized investigative tool in the management of gastrointestinal conditions in children. Biopsies obtained during EGD may pose risk for post‐operative adverse events (AEs), and further understanding of risk is imperative to provide informed consent to families and safe patient care. In particular, the impact of biopsy number and location on the development of AEs has not been studied in pediatric patients. We prospectively assessed for AEs by telephone survey 3–7 days after 209 EGDs performed on patients ages 1–21 years over a 1‐year period. Demographic, endoscopic, and histologic data were collected. The most common symptoms reported were throat pain (61%), chest pain (26%), and dysphagia (26%). Binary regression models identified age and pre‐operative symptoms as factors that influenced the likelihood of post‐operative morbidity. Multiple biopsies from 3 different locations of the esophagus did not impact the risk of post‐operative AEs.
Advances in Thyroid Pathology: High Grade Follicular Cell-derived Thyroid Carcinoma and Anaplastic Thyroid Carcinoma
Authors: Xu Bin , Ghossein Ronald A.
Published: October 2022

In the upcoming World Health Organization fifth edition classification of endocrine tumors, there were several major changes related to high grade follicular-derived thyroid carcinoma (HGFCTC) and anaplastic thyroid carcinoma (ATC) based on emerging evidence about the diagnostic criteria clinical behavior, prognostic factors, and molecular signatures of these tumors. In this review, we aim to summarize the major evolutions of HGFCTC and ATC. HGFCTC is a nonanaplastic carcinoma with high grade features (High mitotic count, tumor necrosis). It is subdivided into poorly differentiated thyroid carcinoma diagnosed using the Turin proposal and differentiated high grade thyroid carcinoma. The latter is defined by the presence of the cytoarchitectutal features of well-differentiated thyroid carcinoma (eg, papillae) but harbors elevated mitotic activity and/or tumor necrosis. Poorly differentiated thyroid carcinoma is predominantly RAS-driven and associated with RAI avidity and high propensity for distant metastasis, whereas differentiated high grade thyroid carcinoma is mostly BRAFV600E-driven. ATC may show a wide range of histologic features. Carcinoma of pure squamous phenotype is associated with a high frequency of BRAF V600E mutations and is now considered as a subtype of ATC. There is a stepwise molecular progression from well-differentiated carcinoma to HGFCTC to ATC manifested by 1) early and persistent driver alteration in the MAPK pathway, particularly BRAF V600E and RAS mutations, and 2) gain of secondary aggressive molecular signatures (such as TERT promoter and TP53 mutations) when tumors progress from well-differentiated to high grade to anaplastic carcinoma.
Uterine Tumors Resembling Ovarian Sex Cord Tumors
Authors: Boyraz Baris , Watkins Jaclyn C. , Young Robert H. , Oliva Esther
Published: October 2022

Uterine tumors resembling ovarian sex cord tumors (UTROSCTs), first characterized by Drs Clement and Scully in 1976, are rare neoplasms showing clinical, morphologic, and immunohistochemical overlap with a number of other uterine tumors, most being mesenchymal. Criteria for aggressive behavior are not clearly established. We report 75 tumors from patients ranging from 21 to 84 (mean=52.4) years. Seventy-one patients were treated by hysterectomy and 4 by conservative total excision. Thirty-eight tumors were intramyometrial, 34 submucosal, and 3 cervical; they ranged from 0.6 to 20 (mean=4.9) cm and were typically tan-yellow. Sixty-eight neoplasms were well-circumscribed and 7 had infiltrative borders (4 only minimally). In 56 tumors, a smooth muscle component was intimately admixed with the neoplastic cells (“pseudoinfiltration”; extensive in 29). Architectural patterns included cords (n=53), diffuse (n=51), hollow tubules (n=48), nests (n=38), trabeculae (n=37), retiform (n=23), solid tubules (n=21), pseudoangiomatoid (n=11), pseudopapillary (n=4), and whorled (n=2); typically, more than 1 pattern was seen. Tumor cells were epithelioid (n=62), epithelioid and spindled (n=12), or spindled (n=1) and/or rhabdoid (n=20; extensive in 2). Cytologic atypia was absent to mild in 57, moderate in 16, and moderate to severe in 2 tumors. Fifty-seven UTROSCTs had ≤2mitoses/10 high power fields (HPF), 12 had 3 to 5/10 HPF, and 6 >5/10 HPF. Necrosis was present in 3 and lymphovascular invasion in 1. Tumor cells showed a polyphenotypic immunohistochemical profile (with positivity for sex cord, smooth muscle, and epithelial markers), most commonly inhibin (17/33+) and calretinin (22/31+) positive. Five of 58 patients with follow-up (22 to 192; mean=73.2 mo) had recurrences/metastases from 30 to 144 months, and 2 died of disease. Malignant tumors showed >3 of the following 5 features compared with benign tumors: size >5 cm, at least moderate cytologic atypia, ≥3 mitoses/10 HPF, infiltrative borders, and necrosis. One of the 5 malignant tumors showed an extensive rhabdoid morphology. UTROSCTs are uncommon, show a wide morphologic spectrum, often pose problems in differential diagnosis, and typically have a benign outcome. Rare tumors are associated with late recurrences and a combination of more than 3 of the 5 features listed above predicted aggressive behavior in this series.
Clinical and microbiological characteristics of Staphylococcus lugdunensis
Authors: Cronin Katie M. , Moso Michael A. , Chan Eddie , Bond Katherine A.
Published: October 2022

Purpose of review

This review provides an update on recent findings about the clinical and microbiological characteristics of Staphylococcus lugdunensis.

Recent findings

European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) differ in their methodology and breakpoints for the detection of penicillin and oxacillin resistance in S. lugdunensis. The EUCAST method for beta-lactamase detection recommends a 1-unit penicillin disk and has demonstrated superior performance compared to the 10-unit penicillin disk recommended by CLSI. A similar outcome has been previously reported in Staphylococcus aureus. In addition, there is emerging oxacillin resistance in some geographical areas. Of particular concern is that oxacillin resistance in mecA positive isolates may not be reliably detected by current cefoxitin breakpoints.

Coagulase negative staphylococci are now recognised as a heterogenous group of organisms that do not microbiologically or clinically behave the same way. The spectrum of clinical disease is species dependent and is particularly true for S. lugdunensis, which causes an array of clinical infections like that of S. aureus. Further studies are needed to assess the performance of phenotypic tests to detect resistance, to ensure that appropriate antimicrobial therapy is delivered to patients.
Outcomes of Nocardiosis and Treatment of Disseminated Infection in Solid Organ Transplant Recipients
Authors: Yetmar Zachary A. , Challener Douglas W. , Seville Maria Teresa , Bosch Wendelyn , Beam Elena
Published: October 2022

Background.

Nocardia is an environmental pathogen with a predilection for causing opportunistic infections in immunocompromised patients, including solid organ transplant (SOT) recipients. Although risk factors have been identified for developing nocardiosis in this population, little is known regarding clinical factors resulting in poor outcomes. We evaluated a cohort of SOT recipients with nocardiosis for associations with 12-month mortality.

Methods.

We performed a multicenter retrospective cohort study of adult SOT recipients diagnosed with culture-confirmed nocardiosis from 2000 to 2020. Patients were followed for 12 months after diagnosis, unless abbreviated by mortality. Multivariable Cox regression was performed to analyze associations with 12-month mortality. A subgroup analysis of patients with disseminated nocardiosis was performed to analyze treatment variables.

Results.

A total of 125 SOT recipients met inclusion criteria; 12-month mortality was 16.8%. Liver transplantation (hazard ratio [HR] 3.52; 95% confidence interval [CI] 1.27-9.76) and time from symptom onset to presentation (HR 0.92/d; 95% CI 0.86-0.99) were independently associated with 12-month mortality, whereas disseminated infection was not (HR 1.23; 95% CI 0.49-3.13). No treatment-specific factors were significantly associated with mortality in 33 patients with disseminated nocardiosis, although survivors had a higher rate of linezolid use.

Conclusions.

This study identified 2 independent associations with 12-month mortality, representing demographics and infection severity. Disseminated infection was not independently associated with poor outcomes, and specific sites of infection may be more important than dissemination itself. No treatment-specific factors were associated with mortality, though this analysis was likely underpowered. Further study of treatment strategies based on specific Nocardia syndromes is warranted.
First report of a carbapenemase OXA-48 producing-Hafnia alvei clinical isolate.
Authors: Sevillano Laura , Herrera Cristhian , Valdes Álvaro , de la Hoz Ángela , Cardeñoso Laura , Domingo Diego , Semiglia Maria Auxiliadora
Published: October 2022

Introduction: Carbapenems are usually used in the treatment of infections caused by cephalosporin-resistant Enterobacterales; however, the increase in carbapenem-resistant enterobacterales (CRE) has become one of the most important problems in public health.  Hafnia alvei is associated with intestinal and extraintestinal infections, especially in patients with any chronic disease or some type of inmunosupression. H. alvei is resistant to first-generation aminopenicillins and cephalosporins because of the β-lactamase (Amp C) in their chromosome, the only carbapenem-resistant Hafnia strain described until now was due to the lack of OmpK36 protein that plays an important role in permeability to carbapenems.
  Case presentation: We present the case of a 65 years old male diagnosed with acute lithiasic cholecystitis. The culture of the biliary prosthesis yielded a OXA-48-producing H. alvei that was identified by MALDI-TOF (matrix-assisted laser desorption/ionization-time of flight) mass spectrometry. Carbapenemase production was detected by immunochromatography and confirmed by sequencing.
Conclusion: To our knowledge, this is the first report of OXA-48-producing H. alvei probably obtained by horizontal transference from E. cloacae -OXA-48 isolated in previous samples.
Multivariate variance components analysis uncovers genetic architecture of brain isoform expression and novel psychiatric disease mechanisms
Authors: Kim Minsoo , Vo Daniel D. , Jops Connor T. , Wen Cindy , Patowary Ashok , Bhattacharya Arjun , Yap Chloe X. , Zhou Hua , Gandal Michael J.
Published: October 2022

Multivariate variance components linear mixed models are fundamental statistical models in quantitative genetics, widely used to quantify SNP-based heritability (h2SNP) and genetic correlation (rg) across complex traits. However, maximum likelihood estimation of multivariate variance components models remains numerically challenging when the number of traits and variance components are both greater than two. To address this critical gap, here we introduce a novel statistical method for fitting multivariate variance components models. This method improves on existing methods by allowing for arbitrary number of traits and/or variance components. We illustrate the utility of our method by characterizing for the first time the genetic architecture of isoform expression in the human brain, modeling up to 23 isoforms jointly across ∼900 individuals within PsychENCODE. We find a significant proportion of isoforms to be under genetic control (17,721 of 93,293 isoforms) with substantial shared genetic effects among local (orcis-) relative to distal (ortrans-) genetic variants (medianrg,cisandrg,trans= 0.31 and 0.06). Importantly, we find that 11.6% of brain-expressed genes (2,900 genes) are heritable only at the isoform-level. Integrating these isoform-specific genetic signals with psychiatric GWAS signals uncovers previously hidden psychiatric disease mechanisms. Specifically, we highlight reduced expression of a specificXRN2isoform as the underlying driver of the strongest GWAS signal for autism spectrum disorder. Overall, our method for fitting multivariate variance components models is flexible, widely applicable, and is implemented in the Julia programming language and available online.