bluuebunny/crossref_metadata_2025 huggingface dataset:
Sodium-glucose cotransporter 2 inhibitors antagonize lipotoxicity in human myeloid angiogenic cells and ADP-dependent activation in human platelets: potential relevance to prevention of cardiovascular events
Authors: Spigoni Valentina , Fantuzzi Federica , Carubbi Cecilia , Pozzi Giulia , Masselli Elena , Gobbi Giuliana , Solini Anna , Bonadonna Riccardo C. , Dei Cas Alessandra
Published: April 2020

Background

The clear evidence of cardiovascular benefits in cardiovascular outcome trials of sodium-glucose cotransporter 2 inhibitors (SGLT2i) in type 2 diabetes might suggest an effect on atherosclerotic plaque vulnerability and/or thrombosis, in which myeloid angiogenic cells (MAC) and platelets (PLT) are implicated. We tested the effects of SGLT2i on inflammation and oxidant stress in a model of stearic acid (SA)-induced lipotoxicity in MAC and on PLT activation. The possible involvement of the Na+/H+ exchanger (NHE) was also explored.

Method

MAC and PLT were isolated from peripheral blood of healthy subjects and incubated with/without SGLT2i [empagliflozin (EMPA) and dapagliflozin (DAPA) 1–100 μM] to assess their effects on SA (100 μM)-induced readouts of inflammation, oxidant stress and apoptosis in MAC and on expression of PLT activation markers by flow-cytometry after ADP-stimulation. Potential NHE involvement was tested with amiloride (aspecific NHE inhibitor) or cariporide (NHE1 inhibitor). Differences among culture conditions were identified using one-way ANOVA or Friedman test.

Results

NHE isoforms (1,5–9), but not SGLT2 expression, were expressed in MAC and PLT. EMPA and DAPA (100 μM) significantly reduced SA-induced inflammation (IL1β, TNFα, MCP1), oxidant stress (SOD2, TXN, HO1), but not apoptosis in MAC. EMPA and DAPA (both 1 μM) reduced PLT activation (CD62p and PAC1 expression). SGLT2i effects were mimicked by amiloride, and only partially by cariporide, in MAC, and by both inhibitors in PLT.

Conclusions

EMPA and DAPA ameliorated lipotoxic damage in stearate-treated MAC, and reduced ADP-stimulated PLT activation, potentially via NHE-inhibition, thereby pointing to plaque stabilization and/or thrombosis inhibition as potential mechanism(s) involved in SGLT2i-mediated cardiovascular protection.
Increased production of periplasmic proteins in Escherichia coli by directed evolution of the translation initiation region
Authors: Mirzadeh Kiavash , Shilling Patrick J. , Elfageih Rageia , Cumming Alister J. , Cui Huanhuan L. , Rennig Maja , Nørholm Morten H. H. , Daley Daniel O.
Published: April 2020

Background

Recombinant proteins are often engineered with an N-terminal signal peptide, which facilitates their secretion to the oxidising environment of the periplasm (gram-negative bacteria) or the culture supernatant (gram-positive bacteria). A commonly encountered problem is that the signal peptide influences the synthesis and secretion of the recombinant protein in an unpredictable manner. A molecular understanding of this phenomenon is highly sought after, as it could lead to improved methods for producing recombinant proteins in bacterial cell factories.

Results

Herein we demonstrate that signal peptides contribute to an unpredictable translation initiation region. A directed evolution approach that selects a new translation initiation region, whilst leaving the amino acid sequence of the signal peptide unchanged, can increase production levels of secreted recombinant proteins. The approach can increase production of single chain antibody fragments, hormones and other recombinant proteins in the periplasm of E. coli.

Conclusions

The study demonstrates that signal peptide performance is coupled to the efficiency of the translation initiation region.
Mesenchymal stem cells: a promising way in therapies of graft-versus-host disease
Authors: Zhou Xinyi , Jin Nan , Wang Fei , Chen Baoan
Published: April 2020

It is well acknowledged that allogeneic hematopoietic stem cell transplantation (allo-HSCT) is an effective treatment for numerous malignant blood diseases, which has also been applied to autoimmune diseases for more than a decade. Whereas graft-versus-host disease (GVHD) occurs after allogeneic hematopoietic stem cell transplantation (allo-HSCT) as a common serious complication, seriously affecting the efficacy of transplantation. Mesenchymal stem cells (MSCs) derived from a wealth of sources can easily isolate and expand with low immunogenicity. MSCs also have paracrine and immune regulatory functions, leading to a broad application prospect in treatment and tissue engineering. This review focuses on immunoregulatory function of MSCs, factors affecting mesenchymal stem cells to exert immunosuppressive effects, clinical application of MSCs in GVHD and researches on MSC-derived extracellular vesicles (EVs). The latest research progress on MSC in related fields is reviewed as well. The relevant literature from PubMed databases is reviewed in this article.
Rivaroxaban versus warfarin for treatment and prevention of recurrence of venous thromboembolism in African American patients: a retrospective cohort analysis
Authors: Costa Olivia S. , Thompson Stanley , Ashton Veronica , Palladino Michael , Bunz Thomas J. , Coleman Craig I.
Published: April 2020

Background

African Americans are under-represented in trials evaluating oral anticoagulants for the treatment of acute venous thromboembolism (VTE). The aim of this study was to evaluate the effectiveness and safety of rivaroxaban versus warfarin for the treatment of VTE in African Americans.

Methods

We utilized Optum® De-Identified Electronic Health Record data from 11/1/2012–9/30/2018. We included African Americans experiencing an acute VTE during a hospital or emergency department visit, who received rivaroxaban or warfarin as their first oral anticoagulant within 7-days of the acute VTE event and had ≥1 provider visit in the prior 12-months. Differences in baseline characteristics between cohorts were adjusted using inverse probability-of-treatment weighting based on propensity scores (standard differences < 0.10 were achieved for all covariates). Our primary endpoint was the composite of recurrent VTE or major bleeding at 6-months. Three- and 12-month timepoints were also assessed. Secondary endpoints included recurrent VTE and major bleeding as individual endpoints. Cohort risk was compared using Cox regression and reported as hazard ratios (HRs) with 95% confidence intervals (CIs).

Results

We identified 2097 rivaroxaban and 2842 warfarin users with incident VTE. At 6-months, no significant differences in the composite endpoint (HR = 0.96, 95%CI = 0.75–1.24), recurrent VTE (HR = 1.02, 95%CI = 0.76–1.36) or major bleeding alone (HR = 0.93, 95%CI = 0.59–1.47) were observed between cohorts. Analysis at 3- and 12-months provided consistent findings for these endpoints.

Conclusions

In African Americans experiencing an acute VTE, no significant difference in the incidence of recurrent VTE or major bleeding was observed between patients receiving rivaroxaban or warfarin.
Hippocampal microglial activation triggers a neurotoxic-specific astrocyte response and mediates etomidate-induced long-term synaptic inhibition
Authors: Li Dongliang , Chen Mingming , Meng Tao , Fei Jianchun
Published: April 2020

Background

Accumulating evidence has highlighted the importance of microglial and astrocyte responses in the pathological development of postoperative cognitive dysfunction (POCD). However, the mechanisms involved are not well understood.

Methods

A perioperative neurocognitive disorders (PND) mouse model was generated by administering etomidate, and cognitive function was assessed using the Morris water maze and novel object recognition tests. Excitatory and inhibitory postsynaptic currents were recorded to analyze neuronal activity. In addition, microglia and astrocytes were isolated by magnetic-activated cell sorting, and genes that were activated in these cells were identified using quantitative polymerase chain reaction.

Results

We observed dramatic cognitive impairment at 1 and 3 weeks after etomidate was administered to 18 month-old mice. Microglia and astrocytes isolated from the hippocampus showed significant microglial activation during the early pathological stage (i.e., 1 week after etomidate injection) and an A1-specific astrocyte response during the late pathological stage (i.e., 3 weeks after etomidate injection). Furthermore, when microglia were eliminated before etomidate was injected, the A1-specific astrocyte activation response was significantly reduced, and cognitive function improved. However, when microglia were eliminated after etomidate application, astrocyte activation and cognitive function were not significantly altered. In addition, activating microglia immediately after a sedative dose of etomidate was injected markedly increased A1-specific astrocyte activation and cognitive dysfunction.

Conclusions

A1-specific astrocyte activation is triggered by activated microglia during the initial pathological stage of PND and induces long-term synaptic inhibition and cognitive deficiencies. These results improve our understanding of how PND develops and may suggest therapeutic targets.
Prevalence and associated factors of mental disorders in the nationwide primary care population in Latvia: a cross-sectional study
Authors: Rancans Elmars , Renemane Lubova , Kivite-Urtane Anda , Ziedonis Douglas
Published: April 2020

Background

Mental disorders are common amongst patients in primary care. There are no published studies on the prevalence of mental disorders in primary care patients in Latvia. The purpose of the study was to evaluate the current prevalence of mental disorders in the nationwide Latvian primary care population and to study possible associated factors and comorbidity of mental disorders.

Methods

A cross-sectional study within the framework of the National Research Program BIOMEDICINE 2014–2017 was performed at 24 primary care settings across Latvia. Adult patients seen over a 1-week time period at each facility were invited to participate in the study. Sociodemographic variables (age, sex, education, employment and marital status, place of residence, and ethnicity) were assessed onsite. A Mini-International Neuropsychiatric Interview assessment was conducted over the telephone within 2 weeks after the visit to the general practitioner (GP).

Results

Overall, 1485 individuals completed the interview. The current prevalence of any mental disorder was 37.2% and was significantly greater in women. Mood disorders (18.4%), suicidality (18.6%) and anxiety disorders (15.8%) were the most frequent diagnostic categories. The current prevalence of any mood disorder was associated with being 50–64 years of age, female sex, economically inactive status, divorced or widowed marital status and urban place of residence, whilst any current anxiety disorder was associated with female sex, lower education, and single marital status; however, being of Russian ethnicity and residing in a small city were protective factors. Suicidality was associated with female sex, lower education, unemployment or economically inactive status, being divorced or widowed and residing in a small city. The comorbidity rates between mental disorders varied from 2.9 to 53.3%.

Conclusions

High prevalence rates of mental disorders, comorbidity and certain associated socio-demographic factors were found in primary care settings in Latvia. This highlights the importance of screening for depression and anxiety disorders and suicidal risk assessment by GPs. The results are fundamentally important for integrative medicine, monitoring and promotion of mental healthcare at the primary care level, as well as for healthcare policy and development of strategic plans in Latvia.
Surgery in COVID-19 patients: operational directives
Authors: Coccolini Federico , Perrone Gennaro , Chiarugi Massimo , Di Marzo Francesco , Ansaloni Luca , Scandroglio Ildo , Marini Pierluigi , Zago Mauro , De Paolis Paolo , Forfori Francesco , Agresta Ferdinando , Puzziello Alessandro , D’Ugo Domenico , Bignami Elena , Bellini Valentina , Vitali Pietro , Petrini Flavia , Pifferi Barbara , Corradi Francesco , Tarasconi Antonio , Pattonieri Vittoria , Bonati Elena , Tritapepe Luigi , Agnoletti Vanni , Corbella Davide , Sartelli Massimo , Catena Fausto
Published: April 2020

The current COVID-19 pandemic underlines the importance of a mindful utilization of financial and human resources. Preserving resources and manpower is paramount in healthcare. It is important to ensure the ability of surgeons and specialized professionals to function through the pandemic. A conscious effort should be made to minimize infection in this sector. A high mortality rate within this group would be detrimental.

This manuscript is the result of a collaboration between the major Italian surgical and anesthesiologic societies: ACOI, SIC, SICUT, SICO, SICG, SIFIPAC, SICE, and SIAARTI. We aim to describe recommended clinical pathways for COVID-19-positive patients requiring acute non-deferrable surgical care. All hospitals should organize dedicated protocols and workforce training as part of the effort to face the current pandemic.
Analysis of a radiographic parameter K-line tilt following adjacent two-level anterior cervical discectomy and fusion: a retrospective study
Authors: Lan Zhibin , Wu Zhiqiang , Xu Weihong , Huang Yuming
Published: April 2020

Background

T1s, C2-7 lordosis, and C2-7 sagittal vertical axis (SVA) are the three most important sagittal parameters in the cervical spine. This study was conducted to investigate the relationships between classical sagittal alignment parameters and a new parameter, K-line tilt, and to study the impact of K-line tilt.

Material and methods

A total of 72 patients who underwent adjacent two-level anterior cervical discectomy and fusion (ACDF) were retrospectively analyzed. Radiographic measurements included T1 slope (T1s), C2-7 lordosis, segment angle (SA), C2-7 SVA, and K-line tilt. The Neck Disability Index (NDI) scores were used to evaluate the clinical prognosis. Pearson correlation coefficients were calculated between radiographic measures. Linear regression analysis was used to analyze the relationship between follow-up K-line tilt and NDI.

Results

ΔNDI was positively correlated with ΔT1s (r = 0.620, p < 0.05), ΔC2-7 SVA (r = 0.645, p < 0.05), and ΔK-line tilt (r = 0.702, p < 0.01); ΔK-line tilt was positively correlated with ΔT1s (r = 0.650, p < 0.05), ΔSA (r = 0.269, p < 0.05), and ΔC2-7 SVA (r = 0.293, p < 0.05); ΔT1s was positively correlated with ΔC2-7 lordosis (r = 0.428, p < 0.05), ΔSA (r = 0.631, p < 0.01), and ΔC2-7 SVA (r = 0.235, p < 0.05); ΔC2-7 lordosis was positively correlated with ΔSA (r = 0.666, p < 0.05) and negatively correlated with ΔC2-7 SVA (r = − 0.467, p < 0.01). The preoperative and postoperative K-line tilt values were statistically significant (p < 0.01), increasing from (7.50 ± 6.48)° to (9.95 ± 5.09)°. Preoperative NDI was positively correlated with preoperative C2-7 SVA (r = 0.639, p = 0.011) and K-line tilt (r = 0.516, p = 0.026); follow-up NDI was positively correlated with follow-up T1s (r = 0.664, p = 0.038), C2-7 SVA (r = 0.756, p = 0.004), and K-line tilt (r = 0.832, p = 0.006). The linear regression model showed that when the follow-up K-lint tilt was > 23.75°, NDI scores were > 25 (R2 = 0.737, p = 0.000).

Conclusion

This study showed that the K-line tilt was strongly correlated with the C2-C7 SVA, indicating that the K-line tilt can be used as another cervical parameter to evaluate cervical alignment in adjacent two-level ACDF. K-line tilt is an important parameter similar to the classical parameter C2–C7 SVA. In particular, a K-line tilt greater than 23.75 corresponded to a worse clinical prognosis, which was defined as an NDI score greater than 25.
Nutrition status and functional prognosis among elderly patients with distal radius fracture: a retrospective cohort study
Authors: Nagai Takako , Tanimoto Koji , Tomizuka Yoshiaki , Uei Hiroshi , Nagaoka Masahiro
Published: April 2020

Background

Distal radius fractures (DRF) are common in the elderly and are typically caused falls. Malnutrition has also been identified as a poor prognostic factor in elderly patients with fractures. However, the relationship between nutritional status and subsequent falls and functional prognosis for DRF in the elderly is not clear. The aim of the present study was to investigate the association between nutritional status and functional prognosis in elderly patients with DRF.

Methods

Study participants included 229 outpatients who required surgical treatment for DRF. The patients’ clinical information, including age, sex, body mass index, bone mineral density, geriatric nnutritional risk index (GNRI), total number of drugs being treated with on admission, use of drugs for osteoporosis, comorbidity severity, the Barthel Index (BI), presence of subsequent falls, fracture type, postoperative follow-up period, and Mayo wrist score was reviewed. Subjects were further divided into two groups according to their GNRI: the malnutrition group and the normal group. Propensity score matching was used to confirm factors affecting the BI and subsequent falls.

Results

Thirty-one patients (13.5%) presented with malnutrition before surgery for DRF. According to multiple liner regression analysis, the GNRI positively affected the efficiency of the BI (β = 0.392, 95% confidence interval [CI], 0.001 to 0.351, p = 0.039). Furthermore, on logistic regression analysis, subsequent falls were associated with serum albumin levels (odds ratio = 0.033, 95% CI, 0.002 to 0.477, p = 0.012).

Conclusion

Malnutrition impaired improvement of activities of daily living (ADL) and increased the incidence of subsequent falls. Improvement of nutritional status before DRF surgery may further improve ADL and prevent falls.
Displacement-related factors influencing marital practices and associated intimate partner violence risk among Somali refugees in Dollo Ado, Ethiopia: a qualitative study
Authors: Sharma Vandana , Amobi Adaugo , Tewolde Samuel , Deyessa Negussie , Scott Jennifer
Published: April 2020

Background

Child and forced marriage have negative health consequences including increased risk of intimate partner violence (IPV) for women and girls. War and humanitarian crises may impact decision-making around marriage and risks of IPV for displaced populations. A qualitative study was conducted among Somali refugees in Dollo Ado, Ethiopia to understand the interplay of factors that contribute to IPV and to inform an intervention. This secondary analysis aims to explore the influence of displacement on marital practices and associated IPV risk.

Methods

Interviews and focus group discussions were conducted in 2016 in Dollo Ado, Ethiopia, among Somali women and men living in Bokolmayo refugee camp, host community members, non-governmental staff and service providers, stakeholders, and community and religious leaders (N = 110). Data were transcribed, translated to English, and coded and analyzed thematically using Dedoose software and a codebook developed a priori.

Results

Findings reveal numerous displacement-related factors that led to perceived shifts in marital practices among refugees, including reductions in child and forced marriages. NGO awareness-raising programs and Ethiopian laws prohibiting child marriage as well as increased access to education for girls were reported to have contributed to these changes, despite continued economic hardship and high perceived risk of non-partner sexual violence within the camp and host community. Polygamy was also perceived to have decreased, primarily due to worsening economic conditions. Forced marriage, polygamy and dowry were reported to contribute to physical IPV, and sexual IPV was reported as common in all types of marital unions. However, there was no evidence that changes in these marital practices contributed to any perceived declines in IPV within this context.

Conclusion

Safe access to education for girls should be prioritized in humanitarian settings. Interventions to address child and forced marriage should address gender and social norms. Intimate partner violence prevention programming should include specialized content taking into account marital practices including child and forced marriage and polygamy. Laws recognizing sexual IPV within marital relationships are needed to reduce sexual IPV.
Pre- and post-synaptic roles for DCC in memory consolidation in the adult mouse hippocampus
Authors: Glasgow Stephen D. , Wong Edwin W. , Thompson-Steckel Greta , Marcal Nathalie , Séguéla Philippe , Ruthazer Edward S. , Kennedy Timothy E.
Published: April 2020

The receptor deleted in colorectal cancer (DCC) and its ligand netrin-1 are essential for axon guidance during development and are expressed by neurons in the mature brain. Netrin-1 recruits GluA1-containing α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) and is critical for long-term potentiation (LTP) at CA3-CA1 hippocampal Schaffer collateral synapses, while conditional DCC deletion from glutamatergic neurons impairs hippocampal-dependent spatial memory and severely disrupts LTP induction. DCC co-fractionates with the detergent-resistant component of postsynaptic density, yet is enriched in axonal growth cones that differentiate into presynaptic terminals during development. Specific presynaptic and postsynaptic contributions of DCC to the function of mature neural circuits have yet to be identified. Employing hippocampal subregion-specific conditional deletion of DCC, we show that DCC loss from CA1 hippocampal pyramidal neurons resulted in deficits in spatial memory, increased resting membrane potential, abnormal dendritic spine morphology, weaker spontaneous excitatory postsynaptic activity, and reduced levels of postsynaptic adaptor and signaling proteins; however, the capacity to induce LTP remained intact. In contrast, deletion of DCC from CA3 neurons did not induce detectable changes in the intrinsic electrophysiological properties of CA1 pyramidal neurons, but impaired performance on the novel object place recognition task as well as compromised excitatory synaptic transmission and LTP at Schaffer collateral synapses. Together, these findings reveal specific pre- and post-synaptic contributions of DCC to hippocampal synaptic plasticity underlying spatial memory.
A rare missense variant in APC interrupts splicing and causes AFAP in two Danish families
Authors: Djursby Malene , Wadt Karin , Frederiksen Jane Hübertz , Madsen Majbritt Busk , Berchtold Lukas Adrian , Hasselby Jane Preuss , Willemoe Gro Linno , Hansen Thomas v. O. , Gerdes Anne-Marie
Published: April 2020

Background

We report the first case of a missense variant in the APC gene that interrupts splicing by creating a new cryptic acceptor site. The variant, c.289G>A, p.(Gly97Arg), is located in exon 3, and qualitative and semi-quantitative RNA splicing analysis reveal that the variant results in skipping of the last 70 nucleotides of the exon, which leads to the introduction of a frameshift and a premature stop codon.

Case presentation

The variant was detected in two, apparently unrelated, Danish families with an accumulation of colorectal cancers, colonic adenomas and other cancers. The families both have an attenuated familial adenomatous polyposis phenotype, which is consistent with the association of pathogenic variants in the 5′ end of the gene.

One variant-carrier also had Caroli Disease and a Caroli Disease associated hepatic mucinous cystadenocarcinoma. This is the first description of a person with both Caroli Disease and a pathogenic APC variant, and although the APC variant is not known to be connected to the development of the hepatic malformations in Caroli Disease, it remains unclear whether the variant could have contributed to the carcinogenesis of the liver tumour.

Conclusions

Based on functional and co-segregation data we classify the APC c.289G>A, p.(Gly97Arg) variant as pathogenic (class 5). Our findings emphasize the importance of a functional evaluation of missense variants although located far from the exon-intron boundaries.
Plasmodium vivax HAP2/GCS1 gene exhibits limited genetic diversity among parasite isolates from the Greater Mekong Subregion
Authors: Li Danni , Yu Chunyun , Guo Jian , Wang Yazhou , Zhao Yan , Wang Lin , Soe Myat Thu , Feng Hui , Kyaw Myat Phone , Sattabongkot Jetsumon , Jiang Lubin , Cui Liwang , Zhu Xiaotong , Cao Yaming
Published: April 2020

Background

Antigens expressed in sexual stages of the malaria parasites are targets of transmission-blocking vaccines (TBVs). HAP2/GCS1, a TBV candidate, is critical for fertilization in Plasmodium. Here, the genetic diversity of PvHAP2 was studied in Plasmodium vivax parasite populations from the Greater Mekong Subregion (GMS).

Methods

Plasmodium vivax clinical isolates were collected in clinics from the China-Myanmar border region (135 samples), western Thailand (41 samples) and western Myanmar (51 samples). Near full-length Pvhap2 (nucleotides 13–2574) was amplified and sequenced from these isolates. Molecular evolution studies were conducted to evaluate the genetic diversity, selection and population differentiation.

Results

Sequencing of the pvhap2 gene for a total of 227 samples from the three P. vivax populations revealed limited genetic diversity of this gene in the GMS (π = 0.00036 ± 0.00003), with the highest π value observed in Myanmar (0.00053 ± 0.00009). Y133S was the dominant mutation in the China-Myanmar border (99.26%), Myanmar (100%) and Thailand (95.12%). Results of all neutrality tests were negative for all the three populations, suggesting the possible action of purifying selection. Codon-based tests identified specific codons which are under purifying or positive selections. Wright’s fixation index showed low to moderate genetic differentiation of P. vivax populations in the GMS, with FST ranging from 0.04077 to 0.24833, whereas high levels of genetic differentiation were detected between the China-Myanmar border and Iran populations (FST = 0.60266), and between Thailand and Iran populations (FST = 0.44161). A total of 20 haplotypes were identified, with H2 being the abundant haplotype in China-Myanmar border, Myanmar and Thailand populations. Epitope mapping prediction of Pvhap2 antigen showed that high-score B-cell epitopes are located in the S307-G324, L429-P453 and V623-D637 regions. The E317K and D637N mutations located within S307-G324 and V623-D637 epitopes slightly reduced the predicted score for potential epitopes.

Conclusions

The present study showed a very low level of genetic diversity of pvhap2 gene among P. vivax populations in the Greater Mekong Subregion. The relative conservation of pvhap2 supports further evaluation of a Pvhap2-based TBV.
EPIGENE: genome-wide transcription unit annotation using a multivariate probabilistic model of histone modifications
Authors: Sahu Anshupa , Li Na , Dunkel Ilona , Chung Ho-Ryun
Published: April 2020

Background

Understanding the transcriptome is critical for explaining the functional as well as regulatory roles of genomic regions. Current methods for the identification of transcription units (TUs) use RNA-seq that, however, require large quantities of mRNA rendering the identification of inherently unstable TUs, e.g. miRNA precursors, difficult. This problem can be alleviated by chromatin-based approaches due to a correlation between histone modifications and transcription.

Results

Here, we introduce EPIGENE, a novel chromatin segmentation method for the identification of active TUs using transcription-associated histone modifications. Unlike the existing chromatin segmentation approaches, EPIGENE uses a constrained, semi-supervised multivariate hidden Markov model (HMM) that models the observed combination of histone modifications using a product of independent Bernoulli random variables, to identify active TUs. Our results show that EPIGENE can identify genome-wide TUs in an unbiased manner. EPIGENE-predicted TUs show an enrichment of RNA Polymerase II at the transcription start site and in gene body indicating that they are indeed transcribed. Comprehensive validation using existing annotations revealed that 93% of EPIGENE TUs can be explained by existing gene annotations and 5% of EPIGENE TUs in HepG2 can be explained by microRNA annotations. EPIGENE outperformed the existing RNA-seq-based approaches in TU prediction precision across human cell lines. Finally, we identified 232 novel TUs in K562 and 43 novel cell-specific TUs all of which were supported by RNA Polymerase II ChIP-seq and Nascent RNA-seq data.

Conclusion

We demonstrate the applicability of EPIGENE to identify genome-wide active TUs and to provide valuable information about unannotated TUs. EPIGENE is an open-source method and is freely available at:https://github.com/imbbLab/EPIGENE.
Associated factors of poor treatment outcomes in patients with giant cell arteritis: clinical implication of large vessel lesions
Authors:   Japan Research Committee of the Ministry of Health, Labour, and Welfare for Intractable Vasculitis (JPVAS), Sugihara Takahiko , Hasegawa Hitoshi , Uchida Haruhito A. , Yoshifuji Hajime , Watanabe Yoshiko , Amiya Eisuke , Maejima Yasuhiro , Konishi Masanori , Murakawa Yohko , Ogawa Noriyoshi , Furuta Shunsuke , Katsumata Yasuhiro , Komagata Yoshinori , Naniwa Taio , Okazaki Takahiro , Tanaka Yoshiya , Takeuchi Tsutomu , Nakaoka Yoshikazu , Arimura Yoshihiro , Harigai Masayoshi , Isobe Mitsuaki
Published: April 2020

Background

Relapses frequently occur in giant cell arteritis (GCA), and long-term glucocorticoid therapy is required. The identification of associated factors with poor treatment outcomes is important to decide the treatment algorithm of GCA.

Methods

We enrolled 139 newly diagnosed GCA patients treated with glucocorticoids between 2007 and 2014 in a retrospective, multi-center registry. Patients were diagnosed with temporal artery biopsy, 1990 American College of Rheumatology classification criteria, or large vessel lesions (LVLs) detected by imaging based on the modified classification criteria. Poor treatment outcomes (non-achievement of clinical remission by week 24 or relapse during 52 weeks) were evaluated. Clinical remission was defined as the absence of clinical signs and symptoms in cranial and large vessel areas, polymyalgia rheumatica (PMR), and elevation of C-reactive protein (CRP) levels. A patient was determined to have a relapse if he/she had either one of the signs and symptoms that newly appeared or worsened after achieving clinical remission. Re-elevation of CRP without clinical manifestations was considered as a relapse if other causes such as infection were excluded and the treatment was intensified. Associated factors with poor treatment outcomes were analyzed by using the Cox proportional hazard model.

Results

Cranial lesions, PMR, and LVLs were detected in 77.7%, 41.7%, and 52.5% of the enrolled patients, respectively. Treatment outcomes were evaluated in 119 newly diagnosed patients who were observed for 24 weeks or longer. The mean initial dose of prednisolone was 0.76 mg/kg/day, and 29.4% received any concomitant immunosuppressive drugs at baseline. Overall, 41 (34.5%) of the 119 patients had poor treatment outcomes; 13 did not achieve clinical remission by week 24, and 28 had a relapse after achieving clinical remission. Cumulative rates of the events of poor treatment outcomes in patients with and without LVLs were 47.5% and 17.7%, respectively. A multivariable model showed the presence of LVLs at baseline was significantly associated with poor treatment outcomes (adjusted hazard ratio [HR] 3.54, 95% CI 1.52–8.24, p = 0.003). Cranial lesions and PMR did not increase the risk of poor treatment outcomes.

Conclusion

The initial treatment intensity in the treatment algorithm of GCA could be determined based upon the presence or absence of LVLs detected by imaging at baseline.
Proof-of-concept trial of the combination of lactitol with Bifidobacterium bifidum and Lactobacillus acidophilus for the eradication of intestinal OXA-48-producing Enterobacteriaceae
Authors: Ramos-Ramos Juan Carlos , Lázaro-Perona Fernando , Arribas José Ramón , García-Rodríguez Julio , Mingorance Jesús , Ruiz-Carrascoso Guillermo , Borobia Alberto M. , Paño-Pardo José Ramón , Herruzo Rafael , Arnalich Francisco
Published: April 2020

Background

The major reservoir of carbapenemase-producing Enterobacteriaceae (CPE) is the gastrointestinal tract of colonized patients. Colonization is silent and may last for months, but the risk of infection by CPE in colonized patients is significant.

Methods

Eight long-term intestinal carriers of OXA-48-producing Enterobacteriaceae (OXA-PE) were treated during 3 weeks with daily oral lactitol (Emportal®), Bifidobacterium bifidum and Lactobacillus acidophilus (Infloran®). Weekly stool samples were collected during the treatment period and 6 weeks later. The presence of OXA-PE was investigated by microbiological cultures and qPCR.

Results

At the end of treatment (EoT, secondary endpoint 1), four of the subjects had negative OXA-PE cultures. Three weeks later (secondary endpoint 2), six subjects were negative. Six weeks after the EoT (primary endpoint), three subjects had negative OXA-PE cultures. The relative intestinal load of OXA-PE decreased in all the patients during treatment.

Conclusions

The combination of prebiotics and probiotics was well tolerated. A rapid reduction on the OXA-PE intestinal loads was observed. At the EoT, decolonization was achieved in three patients.

Clinical Trials Registration: NCT02307383. EudraCT Number: 2014-000449-65.
Differential CpG DNA methylation in peripheral naïve CD4+ T-cells in early rheumatoid arthritis patients
Authors: Pitaksalee R. , Burska A. N. , Ajaib S. , Rogers J. , Parmar R. , Mydlova K. , Xie X. , Droop A. , Nijjar J. S. , Chambers P. , Emery P. , Hodgett R. , McInnes I. B. , Ponchel F.
Published: April 2020

Background

The genetic risk associated with rheumatoid arthritis (RA) includes genes regulating DNA methylation, one of the hallmarks of epigenetic re-programing, as well as many T-cell genes, with a strong MHC association, pointing to immunogenetic mechanisms as disease triggers leading to chronicity. The aim of our study was to explore DNA methylation in early, drug-naïve RA patients, towards a better understanding of early events in pathogenesis.

Result

Monocytes, naïve and memory CD4+T-cells were sorted from 6 healthy controls and 10 RA patients. DNA methylation was assessed using a genome-wide Illumina 450K CpG promoter array. Differential methylation was confirmed using bisulfite sequencing for a specific gene promoter, ELISA for several cytokines and flow cytometry for cell surface markers. Differentially methylated (DM) CpGs were observed in 1047 genes in naïve CD4+T-cells, 913 in memory cells and was minimal in monocytes with only 177 genes. Naive CD4+T-cells were further investigated as presenting differential methylation in the promoter of > 500 genes associated with several disease-relevant pathways, including many cytokines and their receptors. We confirmed hypomethylation of a region of the TNF-alpha gene in early RA and differential expression of 3 cytokines (IL21, IL34 and RANKL). Using a bioinformatics package (DMRcate) and an in-house analysis based on differences in β values, we established lists of DM genes between health and RA. Publicly available gene expression data were interrogated to confirm differential expression of over 70 DM genes. The lists of DM genes were further investigated based on a functional relationship database analysis, which pointed to an IL6/JAK1/STAT3 node, related to TNF-signalling and engagement in Th17 cell differentiation amongst many pathways. Five DM genes for cell surface markers (CD4, IL6R, IL2RA/CD25, CD62L, CXCR4) were investigated towards identifying subpopulations of CD4+T-cells undergoing these modifications and pointed to a subset of naïve T-cells, with high levels of CD4, IL2R, and CXCR4, but reduction and loss of IL6R and CD62L, respectively.

Conclusion

Our data provided novel conceptual advances in the understanding of early RA pathogenesis, with implications for early treatment and prevention.
Ocular microvascular changes in patients with sepsis: a prospective observational study
Authors: Simkiene Jurate , Pranskuniene Zivile , Vitkauskiene Astra , Pilvinis Vidas , Boerma E. Christiaan , Pranskunas Andrius
Published: April 2020

Background

The aim of the study was to detect differences in the conjunctival microcirculation between septic patients and healthy subjects and to evaluate the course of conjunctival and retinal microvasculature in survivors and non-survivors over a 24-h period of time.

Methods

This single-center prospective observational study was performed in mixed ICU in a tertiary teaching hospital. We included patients with sepsis or septic shock within the first 24 h after ICU admission. Conjunctival imaging, using an IDF video microscope, and retinal imaging, using portable digital fundus camera, as well as systemic hemodynamic measurements, were performed at three time points: at baseline, 6 h and 24 h. Baseline conjunctival microcirculatory parameters were compared with healthy controls.

Results

A total of 48 patients were included in the final assessment and analysis. Median APACHE II and SOFA scores were 16[12–21] and 10[7–12], respectively. Forty-four (92%) patients were in septic shock, 48 (100%) required mechanical ventilation. 19 (40%) patients were discharged alive from the intensive care unit. We found significant reductions in all microcirculatory parameters in the conjunctiva when comparing septic and healthy subjects. In addition, we observed a significant lower microvascular flow index (MFI) of small conjunctival vessels during all three time points in non-survivors compared with survivors. However, retinal arteriolar vessels were not different between survivors and non-survivors.

Conclusions

Conjunctival microvascular blood flow was altered in septic patients. In the 24-h observation period conjunctival small vessels had a significantly higher MFI, but no difference in retinal arteriolar diameter in survivors in comparison with non-survivors.

Trial registration NCT04214743, https://www.clinicaltrials.gov. Date of registration: 31 December 2019 – Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT04214743
Investigation of suitability of marbles to standards with inequality expressions and statistical approach using some physical and mechanical properties
Authors: Ozer Ozge , Yalcin Fusun , Tarinc Orhan Kemal , Yalcin Mustafa Gurhan
Published: April 2020

Marble, one of the metamorphic rock formation products, forms by undergoing different physical and chemical processes. The marble samples are tested under laboratory conditions to understand these processes. This study aims to find whether the Akcay region marble (Antalya) is compatible with national and international standards using some physical and mechanical properties. For this purpose, samples were subjected to some laboratory tests (real density, apparent density, total porosity, open porosity, breaking load, compressive strength, flexural strength, rupture energy). A number of statistical findings, linear equations, inequalities, and spatial distribution maps were obtained from the physical and mechanical data found at the end of the laboratory tests. The variables which were found to be statistically significantly correlated according to the results of the correlation analysis were analyzed using regression analysis; then their distributions were explained using linear equations. The spatial distribution maps of the variables reveal the part corresponding to the symbol color ranging between the light green and yellow and covering almost 70% of the area is compliant with both TurkStat and ASTM standards and this is proved using the inequalities.
Assessment of a virtual reality temporal bone surgical simulator: A national face and content validity study
Authors: Compton Evan C. , Agrawal Sumit K. , Ladak Hanif M. , Chan Sonny , Hoy Monica , Nakoneshny Steven C. , Siegel Lauren , Dort Joseph C. , Lui Justin T.
Published: April 2020

Background

Trainees in Otolaryngology–Head and Neck Surgery must gain proficiency in a variety of challenging temporal bone surgical techniques. Traditional teaching has relied on the use of cadavers; however, this method is resource-intensive and does not allow for repeated practice. Virtual reality surgical training is a growing field that is increasingly being adopted in Otolaryngology. CardinalSim is a virtual reality temporal bone surgical simulator that offers a high-quality, inexpensive adjunct to traditional teaching methods. The objective of this study was to establish the face and content validity of CardinalSim through a national study.

Methods

Otolaryngologists and resident trainees from across Canada were recruited to evaluate CardinalSim. Ethics approval and informed consent was obtained. A face and content validity questionnaire with questions categorized into 13 domains was distributed to participants following simulator use. Descriptive statistics were used to describe questionnaire results, and either Chi-square or Fishers exact tests were used to compare responses between junior residents, senior residents, and practising surgeons.

Results

Sixty-two participants from thirteen different Otolaryngology–Head and Neck Surgery programs were included in the study (32 practicing surgeons; 30 resident trainees). Face validity was achieved for 5 out of 7 domains, while content validity was achieved for 5 out of 6 domains. Significant differences between groups ( p-value of < 0.05) were found for one face validity domain (realistic ergonomics, p = 0.002) and two content validity domains (teaching drilling technique, p = 0.011 and overall teaching utility, p = 0.006). The assessment scores, global rating scores, and overall attitudes towards CardinalSim, were universally positive. Open-ended questions identified limitations of the simulator.

Conclusion

CardinalSim met acceptable criteria for face and content validity. This temporal bone virtual reality surgical simulation platform may enhance surgical training and be suitable for patient-specific surgical rehearsal for practicing Otolaryngologists.
Bridging the gap between low-frequency and very-low-frequency earthquakes
Authors: Masuda Koki , Ide Satoshi , Ohta Kazuaki , Matsuzawa Takanori
Published: April 2020

Slow earthquakes that are observed in the > 1 Hz frequency band are called tectonic tremor or low-frequency earthquakes (LFEs) and those in the 0.01–0.10 Hz band are called very-low-frequency earthquakes (VLFEs). These two phenomena are separated by large microseismic noise at 0.1–1.0 Hz. However, recent observations of the signal in this microseismic frequency band accompanying LFEs and VLFEs in the shallow part of the Nankai subduction zone suggest that LFEs and VLFEs are parts of the same broadband phenomenon, “broadband slow earthquakes”. Here, we report the observation of slow earthquake signals in the microseismic frequency band in the western Shikoku region of the Nankai subduction zone, Japan, by stacking many seismograms relative to the timing of the high-frequency LFE signals. We relocate LFE events detected by the Japan Meteorological Agency, use these LFE waveforms to construct synthetic templates, perform a matched-filter event detection analysis using these templates, stack the seismograms recorded by broadband high-sensitivity accelerometers relative to the timing of the detections, and compare the amplitude of the stacked waveforms at different frequency bands. The stacked waveforms have a continuous signal in the 0.015625 Hz (64 s) to 8 Hz frequency band, and support the idea that LFEs are just a small part of the broadband slow earthquake spectrum, which extends to the VLFE frequency band. Furthermore, the frequency dependency of the maximum amplitudes in this study is similar to that of slow earthquakes in the Cascadia subduction zone, and this is also explained by a Brownian slow earthquake model. However, the frequency dependency is inconsistent with the omega-square model, which is a model for ordinary earthquakes.
Primary myeloid cell proteomics and transcriptomics: importance of β-tubulin isotypes for osteoclast function
Authors: Guérit David , Marie Pauline , Morel Anne , Maurin Justine , Verollet Christel , Raynaud-Messina Brigitte , Urbach Serge , Blangy Anne
Published: April 2020

Among hematopoietic cells, osteoclasts (OCs) and immature dendritic cells (DCs) are closely related myeloid cells with distinct functions: OCs participate skeleton maintenance while DCs sample the environment for foreign antigens. Such specificities rely on profound modifications of gene and protein expression during OC and DC differentiation. We provide global proteomic and transcriptomic analyses of primary mouse OCs and DCs, based on original stable isotope labeling with amino acids in cell culture (SILAC) and RNAseq data. We established specific signatures for OCs and DCs, including genes and proteins of unknown functions. In particular, we showed that OCs and DCs have the same α- and β-tubulin isotype repertoire but that OCs express much more of the β tubulin isotype Tubb6 (also known as TBB6). In both mouse and human OCs, we demonstrate that elevated expression of Tubb6 in OCs is necessary for correct podosomes organization and thus for the structure of the sealing zone, which sustains the bone resorption apparatus. Hence, lowering Tubb6 expression hinders OC resorption activity. Overall, we highlight here potential new regulators of OC and DC biology, and illustrate the functional importance of the tubulin isotype repertoire in the biology of differentiated cells.
Adoption and uptake of the lateral flow urine LAM test in countries with high tuberculosis and HIV/AIDS burden: current landscape and barriers
Authors: Singhroy Diane N. , MacLean Emily , Kohli Mikashmi , Lessem Erica , Branigan David , England Kathleen , Suleiman Khairunisa , Drain Paul K. , Ruhwald Morten , Schumacher Samuel , Denkinger Claudia M. , Waning Brenda , Van Gemert Wayne , Pai Madhukar
Published: April 2020

Background: Since 2015, the World Health Organization (WHO) has recommended a commercially available lateral-flow urine LAM test (Alere-LAM) to assist in the diagnosis of tuberculosis (TB) in severely ill people living with HIV (PLHIV). The test can rapidly detect TB in severely ill PLHIV and can identify PLHIV most at-risk of death, leading to mortality reductions. However, its uptake in countries with high burdens of TB and HIV has been slow. To assess the current use landscape and identify barriers to the adoption of Alere-LAM, we conducted a questionnaire-based study in 31 high TB and HIV/AIDS burden countries.

Methods: Between November 2018 and December 2019, we collected responses to a semi-structured questionnaire that had been emailed to staff and affiliates of National TB Programs or HIV/AIDS Programs, Ministries of Health, and TB or HIV institutes of 31 high TB/HIV burden countries. Questions concerned country policies, adoption, and current use of Alere-LAM testing, as well as testing algorithms and barriers preventing Alere-LAM uptake.

Results: We received questionnaire responses from 24 out of 31 (77%) high TB/HIV burden countries. Of these 24 countries, 11 (46%) had adopted Alere-LAM policies, with only five (21%) countries currently using Alere-LAM testing. Testing algorithms were generally aligned with WHO recommendations. Fifteen countries (63%) said they were planning to implement Alere-LAM testing in the near future. The most commonly cited constraint to adoption and implementation was budget limitations. Additional barriers to Alere-LAM implementation included lack of country-specific data and piloting, administrative hurdles such as regulatory agency approval, lack of coordination between National TB and HIV programs, and small perceived patient population.

Conclusion: Responses to our questionnaire demonstrate the persistent gap between country-level policy and real-world use of Alere-LAM, as well as specific barriers that must be addressed to scale-up testing in PLHIV.