bluuebunny/crossref_metadata_2025 huggingface dataset:
A comprehensive bioinformatics analysis of FOXP3 in nonsmall cell lung cancer
Authors: Zhu Jianfei , Li Zhenzhen , Chen Jie , Li Wensheng , Wang Hongtao , Jiang Tao , Ma Yu
Published: December 2022

Fork head box p3 (FOXP3), the specific transcription factors of Tregs, not only in Tregs, but also expressed in cancer cells of certain malignant tumors. The histological positioning of FOXP3 in nonsmall cell lung cancer (NSCLC) and its biological significance are still unclear. This study aims to clarify the biological function of FOXP3 in NSCLC through bioinformatics analysis. Tumor immune estimation resource database was used to analyze the mRNA expression of FOXP3 in pan cancer, and to analyze the correlation between FOXP3 expression and tumor microenvironment cell infiltration. Overall survival and disease-free survival analyses were performed using a Kaplan–Meier plotter. Immunohistochemistry staining of FOXP3 was performed using human protein atalas (HPA) database, and immunofluorescence (IF) staining was used to verify gene expression and identify cell types. Protein–protein interaction (PPI) networks were drawn using STRING and visualized by Cytoscape. The functional and pathway enrichment analysis of FOXP3 used the DAVID database. In NSCLC, whether it is lung squamous cell carcinoma (P < .001) or lung adenocarcinoma (P < .001), FOXP3 is highly expressed in cancer tissue compared with normal tissue. Immunohistochemistry results showed that FOXP3 was mainly expressed in Tregs, but not in lung cancer tissues. IF staining showed that FOXP3 and CD3 (a marker of T cells) were co-expressed in immune cells. Moreover, survival analysis showed that high FOXP3 expression could be used as a predictor of poor overall survival (HR: 1.25, P = .00065) and disease-free survival (HR: 1.88, P = 1.1E-10) in patients with NSCLC. Next, we identified an important module containing 11 genes in the PPI network, including JUN, NFATC, STAT3, IRF4, IL2, IFGN, CTLA4, TNFRSF18, IL2A, KAT5, and FOXP3. KEGG signaling pathway was enriched in T cell receptor signaling pathway, Jak-STAT signaling pathway, cytokine–cytokine receptor interaction. Finally, we observed that FOXP3 expression correlated with infiltration of CD8 + T cells (R = 0.276, P = 5.90E−10), CD4 + T cells (R = 0.643, P = 6.81E−58), neutrophils (R = 0.525, P = 1.57E−35), and dendritic cells (R = 0.608, P = 1.35E−50) in lung adenocarcinoma, the same results were observed in lung squamous cell carcinoma. The infiltration of FOXP3-positive Tregs might promote the malignant progression of NSCLC, and targeted intervention of Tregs may be a potential treatment option for patients with NSCLC.
Neonatal maple syrup urine disease case report and literature review
Authors: Liu Qiao , Li Fang , Zhou Jingjing , Liu Xiaoyu , Peng Jidong , Gong Lianggeng
Published: December 2022

Rationale:

The main clinical symptoms of maple syrup urine disease (MSUD) are dehydration, acidosis, nervous system symptoms and intellectual disability. The brain imaging findings were mainly caused by cytotoxic edema. The lesions usually occur at the site consistent with the myelination process of normal neonates. The distribution is mostly symmetric, and the diffusion is obviously limited.

Patient concerns:

Herein, we report a rare case of an 8-day-old female patient who presented with abnormal symptoms, such as difficulty eating, convulsions, slow reaction, difficulty in correcting hypoglycemia and severe metabolic disorders. Brain magnetic resonance imaging (MRI) revealed abnormal signal intensity mainly involving the brainstem, cervical spinal cord, bilateral cerebellar hemispheres, basal ganglia, thalamus, precentral gyrus, and postcentral gyrus with characteristic hyperintensity on diffusion-weighted imaging (DWI) sequence. MSUD is rarely reported, while cervical spinal cord involvement is extremely rare.

Diagnoses:

Blood tandem mass spectrometry, urine organic acid detection, and genetic disease overall genetic tests were performed to further confirm the diagnosis of MSUD.

Interventions:

Under general anesthesia, she underwent open surgical procedures for liver transplantation.

Outcomes:

The child was in a stable condition after liver transplantation, and the diet was not restricted.

Lessons:

MSUD in neonates is rare. Our case report and literature review was aim to describe the clinic and imaging characteristics of it, and highlight physicians must be aware of this entity in newborns so as to reduce misdiagnosis due to unfamiliarity.
Effects of high-intensity interval training versus moderate-intensity continuous training on blood pressure in patients with hypertension: A meta-analysis
Authors: Li Lei , Liu Xuan , Shen Fei , Xu Naxin , Li Yun , Xu Kun , Li Junping , Liu Yong
Published: December 2022

Background:

This meta-analysis aimed to compare the effects of high-intensity interval training (HIIT) and moderate-intensity continuous training (MICT) on blood pressure in patients with essential hypertension to explore more suitable training.

Methods:

PubMed, EBSCO, Cochrane Library, Web of Science, CNKI, and VIP databases were searched for randomized controlled trials published between January 2002 and November 2022. Weighted mean differences (WMDs) with 95% confidence intervals (CIs) were selected as the effect scale indices for the evaluation of the differences in post-intervention systolic blood pressure (SBP), and diastolic blood pressure (DBP), heart rate, maximum oxygen uptake (VO2max), and flow-mediated vasodilation. All these were compared using Review Manager 5.3 and Stata 14.0.

Results:

A total of 13 randomized controlled trials and 442 patients were included. The meta-analyses revealed no statistically significant differences between HIIT and MICT in improving SBP and DBP in patients with hypertension. Subgroup analyses revealed that HIIT was better than MICT in reducing SBP during daytime monitoring (WMD = −4.14, 95%CI: [−6.98, −1.30], P < .001). In addition, HIIT increased flow-mediated vasodilation more than MICT in hypertensive patients (WMD = 2.75, 95%CI: [0.43, 5.07], P = .02).

Conclusion:

HIIT and MICT have similar effects on the overall resting SBP and DBP in patients with hypertension and prehypertension. However, HIIT is better than MICT at reducing SBP during daytime monitoring. In addition, HIIT can improve vasodilation.
Exploration of restless legs syndrome under the new concept: A review
Authors: Liu Zhao , Guan Ruiqian , Pan Limin
Published: December 2022

Restless leg syndrome (Restless legs syndrome, RLS) is a common neurological disorder. The pathogenesis of RLS remains unknown, and recent pathophysiological developments have shown the contribution of various genetic markers, neurotransmitter dysfunction, and iron deficiency to the disease, as well as other unidentified contributing mechanisms, particularly chronic renal dysfunction. RLS enhancement syndrome is frequently observed in patients with RLS who have received long-term dopamine agonist therapy, manifesting as a worsening of RLS symptoms, usually associated with an increase in the dose of dopamine agonist. Some patients with RLS can adequately control their symptoms with non-pharmacological measures such as massage and warm baths. First-line treatment options include iron supplementation for those with evidence of reduced iron stores, or gabapentin or pregabalin, as well as dopamine agonists, such as pramipexole. Second-line therapies include opioids such as tramadol. RLS seriously affects the quality of life of patients, and because its pathogenesis is unclear, more biological evidence and treatment methods need to be explored.
Association between arsenic exposure and inflammatory cytokines and C-reaction protein: A systematic review and meta-analysis
Authors: Zhang Zheyu , Pi Ruozheng , Luo Jieya , Liu Ji , Zhang Aihua , Sun Baofei
Published: December 2022

Background:

Previous studies have reported controversial results on levels of inflammatory cytokines in patients with arsenic exposure. This study aims to evaluate the associations between arsenic exposure and inflammatory cytokines and C-reaction protein (CRP).

Methods:

We searched the databases including PubMed, Embase, Web of Science, and China national knowledge infrastructure (CNKI) for studies reporting levels of cytokines and CRP in patients with arsenic exposure compared to the controls. The retrieval time was from January 2000 to September 2022.

Results:

13 observational studies involving 1665 arsenic exposed and 1091 unexposed individuals were included. Among these studies, 6 from China, 4 from India, 2 from Bangladesh and 1 from Turkey. Our result showed that interleukin (IL)-6, IL-8, and IL-12 levels were significantly higher in arsenic-exposed individuals compared to the control group, IL-2 level was significantly lower, and Tumor necrosis factor-α, Interferon-γ, CRP, and IL-10 levels were not changed. After sensitivity analyses, tumor necrosis factor-α and Interferon-γ levels were significantly higher in arsenic-exposed individuals compared to the control group. High heterogeneity was detected in most studies.

Conclusion:

Many cytokines (such as IL-6, IL-8, and IL-12) have altered in individuals with arsenic exposure, this indicates arsenic exposure could trigger the cell-mediated inflammatory response. Regular examining immune function (such as inflammatory cytokines) in individuals with the risk of arsenic exposure is important to human health.
Cauda Equina Neuroendocrine Tumors
Authors: Asa Sylvia L. , Mete Ozgur , Schüller Ulrich , Ramani Biswarathan , Mirchia Kanish , Perry Arie
Published: December 2022

The tumor formerly known as “cauda equina paraganglioma” was recently renamed as cauda equina neuroendocrine tumor (CENET) based on distinct biological and genetic properties. Nevertheless, it remains insufficiently understood. For this study, we retrieved CENETs (some previously reported), from the pathology files of 3 institutions; we examined their immunohistochemical profile, including common neuroendocrine tumor–associated hormones and transcription factors. We identified 24 CENETs from 7 female and 17 male adult patients, with a median age of 47 years. Six included neurofilament-positive ganglion cells. All tumors tested were positive for INSM1, synaptophysin, chromogranin A, SSTR2, and CD56 as well as at least 1 keratin (AE1/AE3, CAM5.2); CK7 and CK20 were negative. Glial fibrillary acidic protein was negative, except for peripheral nontumoral elements. S100 protein was variable but mainly expressed in scattered sustentacular cells. All but 1 tumor tested were positive for HOXB13; several stained for SATB2, and all tumors were consistently negative for GATA3. All tumors tested were negative for transcription factors found in various other epithelial neuroendocrine neoplasms including TTF1, CDX2, PIT1, TPIT, SF1, and PAX8; staining for T-brachyury was negative. Four of 5 CENETs tested had at least focal tyrosine hydroxylase reactivity. Serotonin expression was detected in all 21 tumors tested; it was diffusely positive in 5 and had variable positivity in the remainder. A few tumors had scattered cells expressing gastrin, calcitonin, pancreatic polypeptide, and peptide YY, while glucagon, adrenocorticotropic hormone, and monoclonal carcinoembryonic antigen were negative. PSAP expression was found focally in 4 of 5 tumors examined. SDHB was consistently intact; ATRX was intact in 14 tumors and showed only focal loss in 3. The median Ki-67 labeling index was 4.5% (range: 1% to 15%). We conclude that CENET represents a distinct neuroendocrine neoplasm; the subset with ganglion cells qualifies for designation as composite gangliocytoma/neuroma-neuroendocrine tumor (CoGNET) as defined in the 2022 WHO classification of neuroendocrine neoplasms. In addition to INSM1, chromogranin, synaptophysin, and keratins, the most characteristic finding is nuclear HOXB13 expression; a subset also express SATB2. Serotonin is the most common hormone expressed. The cytogenesis and pathogenesis of these lesions remains unclear.
Pregnancy Outcomes in Women With Rheumatoid Arthritis
Authors: Sim Bernice L. , Daniel Rohan Suresh , Hong Sam S. , Matar Reem H. , Ganiel Imri , Nakanishi Hayato , Mansour Rania , Than Christian A. , Alrahmani Layan
Published: December 2022

Rheumatoid arthritis (RA) is a chronic inflammatory rheumatic disease affecting multiple joints and can also be a systemic widespread, affecting major organs. Rheumatoid arthritis is associated with greater adverse maternal and neonatal outcomes in comparison to the general obstetric population. This systematic review and meta-analysis aims to investigate the pregnancy outcomes in RA patients in comparison to the general pregnant population.

Nine studies involving 11,999 RA patients met the eligibility criteria with 9,921,808 controls. Rheumatoid arthritis patients were compared with their control counterparts according to random-effects model statistical analysis.

We searched databases from inception to September 8, 2021. Eligible studies reported maternal outcomes (preeclampsia, cesarean delivery, and preterm delivery) and/or neonatal outcomes. Data were pooled across using random-effects model. Subgroup analysis was conducted on RA patients alone. The review was registered prospectively with PROSPERO (CRD42021250521).

In terms of maternal outcomes, there was an increased rate of cesarean delivery (odds ratio [OR], 1.55), preeclampsia (OR, 1.61), and preterm delivery (OR, 1.83) in RA patients compared with their control counterparts. In terms of neonatal outcomes, a higher rate of lower gestational weight (mean difference [MD], −0.19 kg), requirement for neonate intensive care unit admission (OR, 1.34), and stillbirths (OR, 1.99) were observed in RA patients compared with the controls. A subgroup analysis of 4 studies involving only RA patients (n = 3761) was conducted. A total of 33.2% of patients had a cesarean delivery, 7.3% had preeclampsia, 14.8% had a preterm delivery, and 9.5% of neonates had low birth weight.

Compared with the general pregnant population, women with RA tend to have a higher risk of maternal and neonatal complications. As a result, this study hopes to increase awareness into the importance of counseling and managing RA patients.
IVABRADINE-INDUCED HEART RATE REDUCTION INCREASES THE SEVERITY OF POSTRESUSCITATION MYOCARDIAL DYSFUNCTION IN A RAT MODEL OF CARDIOPULMONARY RESUSCITATION
Authors: Hu Zhangle , Gao Shan , Yang Jin , Xu Banglong , Tang Wanchun , Bradley Jennifer L. , Peberdy Mary Ann , Ornato Joseph P.
Published: December 2022

Aims: A rapid heart rate (HR) that occurs after cardiopulmonary resuscitation (CPR) is a short-term compensatory mechanism preserving cardiac output. However, if of long duration, it is unfavorable for myocardial function postresuscitation because of disrupted balance between myocardial oxygen supply and demand. This raises the assumption that such a sustained fast HR should be regulated. The present study aimed to investigate the follow-on effect of ivabradine (a specific inhibitor of the If current of the sinoatrial node)–induced HR reduction (HRR) on postresuscitation myocardial function in a rat model of CPR. Methods and results: Six minutes of ventricular fibrillation and 8 min of CPR were performed on Sprague-Dawley rats. All 32 resuscitated animals were then randomized into saline and ivabradine groups, each group having nonsurvival and survival subgroups (n = 8 each). Saline or ivabradine (0.5 mL/kg) was administered at 1 h postresuscitation. Heart rate, myocardial function as expressed by cardiac output, ejection fraction, and myocardial performance index were assessed at baseline and hourly from 1 to 5 h postresuscitation. Heart rate variability was analyzed at baseline and at 1, 3, and 5 h postresuscitation. Serum epinephrine and cardiac troponin I at baseline and at 1, 3, and 5 h postresuscitation in nonsurvival subgroup were measured. Survival duration in the survival subgroup was observed. The baseline HR was approximately 390 beats/min (bpm). After resuscitation, an average increase of Δ ≈ +15 bpm (relative ratio ≈ +3.8%) with a resultant HR of 405 bpm lasting more than 5 h occurred. Ivabradine group achieved a steady HRR of Δ ≈ −30 bpm (relative ratio ≈ −7.4%) as compared with saline group (P < 0.01). Postresuscitation myocardial function was significantly worse in the ivabradine group (all P < 0.01). Heart rate variability was significantly impaired in the ivabradine group (all P < 0.05). Serum cardiac troponin I and epinephrine concentration were significantly higher in the ivabradine group (all P < ?0.01). Survival duration was significantly shortened in the ivabradine group as compared with the saline group (388 vs. 526 min, P < ?0.01). Conclusions: Ivabradine-induced HRR increases the severity of postresuscitation myocardial dysfunction and shortens survival duration in a rat model of CPR.
HIGH HEPARANASE LEVEL IN SURVIVORS OF COVID-19 — INDICATOR OF VASCULAR AND PULMONARY RECOVERY?
Authors: Neb Holger , Talbot Steven R. , Ruskowski Katharina , Brkic Djurdjina , Sonntagbauer Michael , Adam Elisabeth H. , von Knethen Andreas , Zacharowski Kai , Heinicke Ulrike
Published: December 2022

Background: Severe progression of coronavirus disease 2019 (COVID-19) causes respiratory failure and critical illness. Recently, COVID-19 has been associated with heparanase (HPSE)-induced endothelial barrier dysfunction and inflammation, so called endothelitis, and therapeutic treatment with heparin or low-molecular-weight heparin (LMWH) targeting HPSE has been postulated. Because, up to this date, clinicians are unable to measure the severity of endothelitis, which can lead to multiorgan failure and concomitant death, we investigated plasma levels of HPSE and heparin-binding protein (HBP) in COVID-19 intensive care patients to render a possible link between endothelitis and these plasma parameters. Therefore, a prospective prolonged cohort study was conducted, including 47 COVID-19 patients from the intensive care unit. Plasma levels of HPSE, and HBP were measured daily by enzyme-linked immunosorbent assay in survivors (n = 35) and nonsurvivors (n = 12) of COVID-19 from admission until discharge or death. All patients were either treated with heparin or LMWH, aiming for an activated partial thromboplastin time of ≥60 seconds or an anti-Xa level of >0.8 IU/mL using enoxaparin, depending on the clinical status of the patient (patients with extracorporeal membrane oxygenation or >0.1 μg/kg/min noradrenaline received heparin, all others enoxaparin). Results: We found significantly higher plasma levels of HPSE and HBP in survivors and nonsurvivors of COVID-19, compared with healthy controls. Still, interestingly, plasma HPSE levels were significantly higher (P < 0.001) in survivors compared with nonsurvivors of COVID-19. In contrast, plasma HBP levels were significantly reduced (P < 0.001) in survivors compared with nonsurvivors of COVID-19. Furthermore, when patients received heparin, they had significantly lower HPSE (P = 2.22e − 16) and significantly higher HBP (P = 0.00013) plasma levels as when they received LMWH. Conclusion: Our results demonstrated that patients, who recover from COVID-19–induced vascular and pulmonary damage and were discharged from the intensive care unit, have significantly higher plasma HPSE level than patients who succumb to COVID-19. Therefore, HPSE is not suitable as marker for disease severity in COVID-19 but maybe as marker for patient's recovery. In addition, patients receiving therapeutic heparin treatment displayed significantly lower heparanse plasma level than upon therapeutic treatment with LMWH.
Incidence and Risk Factors of Feeding Intolerance in Adult Patients Given Enteral Nutrition Therapy After Liver Transplant
Authors: Duan Yuyu , Zhou Qing , Dang Wen , Ma Yingying , Huang Lei , Hu Ailing
Published: December 2022

This study aimed to describe the occurrence of feeding intolerance (FI) in adult patients given enteral nutrition (EN) during the first week after liver transplant and investigate the risk factors of FI. A total of 320 adult patients were enrolled and the incidence of FI was 50.3%. There are 5 independent risk factors for FI in these patients: average EN infusion rate, length of time to initiate EN, use of mechanical ventilation, use of sedatives or analgesics, and intraoperative fluid balance. Appropriate EN regimens and clinical treatments should be taken into consideration to prevent FI for these patients.
Follow-up of Patients Receiving Home Parenteral Nutrition With a Competent Home Infusion Nurse Decreases the Prevalence of Catheter Infections
Authors: Eşme Mert , Balcı Cafer , Öz Gökşen , Tamer Fatma , Doğancı Nilgün , Akçay Kezban , Ataç Şermin , Kelleci Burcu , Akıncı Seda Banu , Topeli Arzu , Abbasoğlu Osman , Halil Meltem
Published: December 2022

High rates of infection are reported in patients receiving home parenteral nutrition (HPN). The aims of this study were to investigate the effect of the support of a competent home infusion nurse on catheter-related infection rates among patients receiving HPN as well as to investigate the effect of HPN on quality of life (QOL). Seventeen HPN patients older than 18 years were visited twice weekly by a competent home infusion nurse, and QOL tests were performed over a 2-year period. The patients were evaluated regularly for signs of catheter-related infections and other complications. The catheter infection rate was found to be 1.23 per 1000 catheter-days, and QOL scores remained stable. Involvement of an experienced nurse may help implement HPN with low catheter-related infection rates.
Cytokine signaling converging onIL11in ILD fibroblasts provokes aberrant epithelial differentiation signatures
Authors: Kastlmeier Miriam T. , Rodriguez Erika Gonzalez , Cabanis Phoebe , Guenther Eva M. , König Ann-Christine , Han Lianyong , Hauck Stefanie M. , See Fenja , Asgharpour Sara , Bukas Christina , Burgstaller Gerald , Piraud Marie , Lehmann Mareike , Hatz Rudolf A. , Behr Jürgen , Stoeger Tobias , Hilgendorff Anne , Voss Carola
Published: December 2022

Interstitial lung disease (ILD) is a heterogenous group of lung disorders where destruction and incomplete regeneration of the lung parenchyma often results in persistent architectural distortion of the pulmonary scaffold. Continuous mesenchyme-centered, disease-relevant signaling likely initiates and perpetuates the fibrotic remodeling process, specifically targeting the epithelial cell compartment, thereby destroying the gas exchange area.

With the aim of identifying functionally relevant mediators of the lung mesenchymal-epithelial crosstalk that hold potential as new targets for therapeutic strategies, we developed a 3D organoid co-culture model based on human induced pluripotent stem cell-derived alveolar epithelial type 2 cells that form alveolar organoids in presence of lung fibroblasts from ILD patients as well as a control cell line (IMR-90). While organoid formation capacity and size was comparable in the presence of ILD or control lung fibroblasts, metabolic activity was significantly increased in ILD co-cultures. Alveolar organoids cultured with ILD fibroblasts further demonstrated reduced stem cell function as reflected by reducedSurfactant Protein Cgene expression together with an aberrant basaloid-prone differentiation program indicated by elevatedCadherin 2, Bone Morphogenic Protein 4andVimentintranscription.

In order to screen for key mediators of the misguided mesenchymal-to-epithelial crosstalk with a focus on disease-relevant inflammatory processes, we used mass spectrometry and characterized the secretome of end stage ILD lung fibroblasts in comparison to non-chronic lung disease (CLD) patient fibroblasts. Out of the over 2000 proteins detected by this experimental approach, 47 proteins were differentially abundant comparing ILD and non-CLD fibroblast secretome.

The ILD secretome profile was dominated by chemokines, includingCXCL1, CXCL3, andCXCL8, interfering with growth factor signaling orchestrated byInterleukin 11 (IL11), steering fibrogenic cell-cell communication, and proteins regulating extracellular matrix remodeling including epithelial-to-mesenchymal transition. When in turn treating alveolar organoids withIL11, we recapitulated the co-culture results obtained with primary ILD fibroblasts including changes in metabolic activity.

In summary, we identified mediators likely contributing to the disease-perpetuating mesenchymal-to-epithelial crosstalk in ILD. In our alveolar organoid co-cultures, we were able to highlight the importance of fibroblast-initiated aberrant epithelial differentiation and confirmedIL11as a key player in ILD pathogenesis by unbiased ILD fibroblast secretome analysis.

Abstract Figure
The utility of quantitative D-Dimer assay as a biomarker in the diagnosis and exclusion of Cerebral Venous Sinus Thrombosis
Authors: Soni Dipesh , Pannu Ashok Kumar , Saroch Atul , Bhatia Vikas , Ahluwalia Jasmina , Singh Rajveer , Jain Arihant
Published: December 2022

Thrombotic disorders are characterized by the presence of elevated levels of detectable fibrin degradation products in the blood. The utility and sensitivity of quantitative D-Dimer assay to rule out the diagnosis of deep vein thrombosis is well established. We extrapolated this principle to evaluate the utility of D-Dimer assay in exclusion of cerebral venous sinus thrombosis (CVST). CVST is an important cause of cerebrovascular accidents in young patients and the residual neurological deficits can be minimized if correct therapy, i.e., anticoagulation is instituted in a timely manner. As advanced imaging modalities that are required for the diagnosis of CVST might not be readily available everywhere, it is important to have a sensitive biomarker which can guide clinicians to rule out the diagnosis with a reasonable confidence. We evaluated the patients admitted at a tertiary care center who underwent Computed tomography (CT) Venography/Magnetic resonance (MR) Venography of the brain with the clinical suspicion of CVST. After appropriate exclusion, a quantitative D-Dimer assay was performed in patients who had CVST on CT/MR Venography and was compared with those patients who did not. Receiver operating characteristic (ROC) analysis revealed that quantitative D Dimer had poor diagnostic accuracy for the differentiation of CVST from non CVST cases (Area under the curve = 0.694), but D-Dimer levels of <300 ng/mL had a sensitivity of 90% for ruling out the diagnosis of CVST.
Mental health care in the city of Lubumbashi, Democratic Republic of the Congo: Analysis of demand, supply and operational response capacity of the health district of Tshamilemba
Authors: Mukala-Mayoyo Erick , Criel Bart , Michielsen Joris , Chuy Didier , Coppieters Yves , Chenge Faustin
Published: December 2022

Background

Integrating mental health care into the primary care system is an important policy option in the Democratic Republic of the Congo (DRC). From the perspective of the integration of mental health care in district health services, this study analyzed the existing demand and supply of mental health care in the health district of Tshamilemba, which is located in Lubumbashi, the second largest city of the DRC. We critically examined the district’s operational response capacity to address mental health.

Methods

A multimethod cross-sectional exploratory study was carried out. We conducted a documentary review (including an analysis of the routine health information system) from the health district of Tshamilemba. We further organized a survey to which 591 residents responded and conducted 5 focus group discussions with 50 key stakeholders (doctors, nurses, managers, community health workers and leaders, health care users). The demand for mental health care was analyzed through the assessment of the burden of mental health problems and care-seeking behaviors. The mental health care supply available was described. Finally, the district’s operational response capacity was assessed.

Results

Analysis of technical documents indicated that the burden of mental health problems is a major public problem in Lubumbashi. However, the proportion of mental health cases among the general patient population seen in the outpatient curative consultations in the Tshamilemba district remains very low, at an estimated 5.3%. The interviews not only pointed to a clear demand for mental health care but also indicated that there is currently hardly any offer of care available in the district. There are no dedicated psychiatric beds, nor is there a psychiatrist or psychologist available. In this context, the main source of care for people remains traditional medicine.

Conclusion

The gaps in the management of mental health problems constitute a major challenge in the DRC in general and in the health district of Tshamilemba in particular. Testing the feasibility of integrating a basic package of mental health care into existing primary care services is therefore of great relevance. Such a policy may contribute to strengthening the health system and enhancing people’s access to quality mental health care.
Multi-center integrated analysis of non-coding CRISPR screens
Authors: Yao David , Tycko Josh , Oh Jin Woo , Bounds Lexi R. , Gosai Sager J. , Lataniotis Lazaros , Mackay-Smith Ava , Doughty Benjamin R. , Gabdank Idan , Schmidt Henri , Youngworth Ingrid , Andreeva Kalina , Ren Xingjie , Barrera Alejandro , Luo Yunhai , Siklenka Keith , Yardımcı Galip Gürkan ,   The ENCODE4 Consortium, Tewhey Ryan , Kundaje Anshul , Greenleaf William J. , Sabeti Pardis C. , Leslie Christina , Pritykin Yuri , Moore Jill E. , Beer Michael A. , Gersbach Charles A. , Reddy Timothy E. , Shen Yin , Engreitz Jesse M. , Bassik Michael C. , Reilly Steven K.
Published: December 2022

The ENCODE Consortium’s efforts to annotate non-coding,cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes which play a major role in health and disease. Pooled, non-coding CRISPR screens are a promising approach for systematically investigating gene regulatory mechanisms. Here, the ENCODE Functional Characterization Centers report 109 screens comprising 346,970 individual perturbations across 13.3Mb of the genome, using a variety of methods, readouts, and statistical analyses. Across 332 functionally confirmed CRE-gene links, we identify principles for screening endogenous, non-coding elements for causal regulatory mechanisms. Nearly all CREs show strong evidence of open chromatin, and targeting accessibility peak summits is a critical component of our proposed sgRNA design rules. We provide experimental guidelines to accurately detect CREs with variable, often low, transcriptional effects. We discover a previously undescribed DNA strand-bias for CRISPRi in transcribed regions with implications for screen design and analysis. Benchmarking five screen analysis tools, we find CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity sgRNAs. Together, we provide an accessible data resource, predesigned sgRNAs targeting 3,275,697 ENCODE SCREEN candidate CREs, and screening guidelines to accelerate functional characterization of the non-coding genome.
Inflammatory Synovial Fibroblast Culture in 3D Systems: A Comparative Transcriptomic and Functional Study
Authors: Khan Aneesah , Dobre Oana , Wang Yilin , Sartyoungkul Thanutchaporn , Salmeron-Sanchez Manuel , Harnett Margaret H. , Pineda Miguel A.
Published: December 2022

Inflammation is essential for responding to infections and subsequent tissue healing. However, chronic unresolved inflammation can become a serious health problem, as exemplified in the joints during Rheumatoid Arthritis (RA). Why does inflammation persist in RA? The answer could lie with synovial fibroblasts, non-haemopoietic cells that can adopt a pathogenic phenotype that fuels disease progression for years. Critically, targeting local fibroblasts could stop joint inflammation without suppressing systemic immunity. Nevertheless, basic research findings have not been translated to new drugs, perhaps because non-physiological data can be inadvertently generated in 2D cultures. Thus, developing better in vitro platforms is an urgent need in biomedical research. In this work, we sought to understand how distinct 3D environments affect fibroblast-mediated inflammation. Arthritic synovial fibroblasts were expanded and cultured in 2D, 3D rigid scaffolds and engineered hydrogels. The results reveal that SFs are plastic and adopt inflammatory or remission-like phenotypes in response to their surroundings. This work identifies new directions to develop better models for drug testing, and even signposts candidate mechanisms by which to rewire destructive SFs.
ABorrelia burgdorferiLptD Homolog Facilitates Flipping of Surface Lipoproteins Through the Spirochetal Outer Membrane
Authors: He Huan , Pramanik Ankita S. , Swanson Selene K. , Johnson David K. , Florens Laurence , Zückert Wolfram R.
Published: December 2022

Borreliaspirochetes are unique among diderm bacteria in their lack of lipopolysaccharide (LPS) in the outer membrane (OM) and their abundance of surface-exposed lipoproteins with major roles in transmission, virulence, and pathogenesis. Despite their importance, little is known about how surface lipoproteins are translocated through the periplasm and the OM. In this study, we characterizedBorrelia burgdorferiBB0838, a distant homolog of the OM LPS assembly protein LptD. Using a CRISPR interference approach, we showed that BB0838 is essential for cell growth. Upon BB0838 knockdown, sentinel surface lipoprotein OspA was retained in the inner leaflet of the OM, as determined by its inaccessibility toin situproteolysis but its presence in OM vesicles. The secretion, insertion and topology of theB. burgdorferiOM porin P66 remained unaffected. MudPIT quantitative mass spectrometry analysis of theB. burgdorferimembrane-associated proteome further confirmed the selective periplasmic retention of surface lipoproteins under BB0838 knockdown conditions. Alphafold Multimer modeling predicted aB. burgdorferiLptB2FGCAD complex spanning the periplasm. Together, this indicates that BB0838 facilitates the essential terminal step in a distinctive spirochetal lipoprotein secretion pathway that evolved in parallel to the LPS secretion pathway in gram-negative bacteria. Hence, BB0838/LptDBbrepresents an attractive target for novel antimicrobials.
Prefrontal Control of Innate Escape Behavior – A Neural Mechanism of Enhanced Posttraumatic Threat Detection
Authors: Ritter Ami , Habusha Shlomi , Edut Shahaf , Klavir Oded
Published: December 2022

Innate defensive responses, while primarily instinctive, must also be flexible and highly adaptive to changes in risk assessment. As such, efficient innate escape behavior requires intricate processing to minimize reaction time while maximizing the success and adaptivity of the action. The superior colliculus (SC) is a subcortical sensorimotor integration center linking sensory threat information and escape. Adaptive changes in innate escape after learning could take a maladaptive turn after severe stress. Posttraumatic stress disorder (PTSD) is associated with long-term maladaptive changes after exposure to traumatic events, related to enhanced threat detection and reaction. Such long-term modifications are thought to involve the medial prefrontal cortex (mPFC), which is implicated in integrating learned emotional values into decisions that drive actions and behaviors. Here, in a series of experiments, we establish the crucial physiological role of specific mPFC neurons, exerting influence on the SC both directly and indirectly through the basal ganglia, in threat detection and reaction after adversity.
RecView: an interactive R application for viewing and locating recombination positions using pedigree data
Authors: Zhang Hongkai , Hansson Bengt
Published: December 2022

Recombination generates new haplotypes and disconnects linked genes thereby increasing the efficiency of selection and the adaptive potential. Quantifying the recombination landscape,i.e., the recombination rate variation along chromosomes, is important for understanding how evolutionary processes such as selection and drift are acting on genes and chromosomes. Here, we presentRecView, an interactive R application, designed to view and locate recombination positions along chromosomes using whole-genome genotype data of a three-generation pedigree.RecViewvisualises the grandparent-of-origin of all informative alleles along each chromosome of the offspring in the pedigree. It also infers putative recombination positions with two algorithms, one based on change in the proportion of the alleles with specific grandparent-of-origin, and one on the degree of continuity of alleles with the same grandparent-of-origin, along the chromosome. Putative recombination positions are given in base pairs together with an estimated error based on the local density of informative alleles. We demonstrate the applicability ofRecViewusing sequencing data of one 120 Mb-large chromosome of one offspring (and its four grandparents and two parents) of a passerine bird, the great reed warbler (Acrocephalus arundinaceus). On this chromosome, we detected five recombination events, three on the paternal chromosome and two on the maternal chromosome with both algorithms. To evaluate how sensitive the analysis is for SNP density, we downsampled our data to 10% of the original dataset. In conclusion, we provide an easy-to-use and highly effective application for viewing and locating recombination positions along chromosomes in small pedigrees.RecViewand test data are available on GitHub (https://github.com/HKyleZhang/RecView.git).
Oral delivery of GLP-1R agonist by an engineered probiotic yeast strain has anti-obesity effects in mice
Authors: Hedin Karl Alex , Zhang Hongbin , Kruse Vibeke , Rees Vanessa Emily , Bäckhed Fredrik , Greiner Thomas U. , Vazquez-Uribe Ruben , Sommer Morten Otto Alexander
Published: December 2022

Obesity is rapidly increasing within the global population and is one of the leading causes of chronic diseases, including type 2 diabetes (T2D), non-alcoholic fatty liver disease, and cardiovascular diseases. Glucagon-like peptide-1 receptor (GLP-1R) agonists have emerged as promising therapeutic agents for treating T2D and obesity. However, the route of administration of the GLP-1R agonists is currently by injection or high oral dosages of the therapeutic combined with absorption enhancers. Oral delivery of GLP-1R agonists remains the preferred administration route due to convenience and high patient compliance. Thus, strategies to improve the oral delivery of this therapeutic are needed. In this study, we engineered the probiotic yeastSaccharomyces boulardiistrain to produce Exendin-4, a GLP-1R agonist, in the gastrointestinal tract to reduce the adverse effects of diet-induced obesity in male C57BL/6 mice. The biological efficiency of the secreted Exendin-4 fromS. boulardiiwas characterisedex vivoon isolated pancreatic islets, demonstrating induced insulin secretion. Furthermore,in vivocharacterisation of the engineered strain identified a synergistic effect of cold exposure and Sb-Exe4 by successfully inhibiting appetite and promoting body weight loss under cold exposure (8°C). In addition, the combination of cold and Sb-Exe4 improved the glucose and lipid homeostasis in the mice by increasing the circulating glucagon level and reducing the inflammatory marker TNF-α. Our results demonstrate thatS. boulardiican be genetically modified to secrete and deliver active therapeutic GLP-1R agonists in the gastrointestinal tract improving the metabolism of the host.
The circadian clock genebmal1is necessary for co-ordinated circatidal rhythms in the marine isopodEurydice pulchra(Leach)
Authors: Zhang Lin , Green Edward W. , Webster Simon G. , Hastings Michael H. , Wilcockson David C. , Kyriacou Charalambos P.
Published: December 2022

Circadian clocks in terrestrial animals are encoded by molecular feedback loops involving the negative regulators PERIOD, TIMELESS or CRYPTOCHROME2 and positive transcription factors CLOCK and BMAL1/CYCLE. The molecular basis of circatidal (∼12.4 hour) or other lunar-mediated cycles (∼15 day, ∼29 day), widely expressed in coastal organisms, is unknown. Disrupting circadian clockworks does not appear to affect lunar-based rhythms suggesting a molecular independence of the two cycles. Nevertheless, pharmacological inhibition of casein kinase 1 (CK1) that targets PERIOD stability in mammals and flies, affects both circadian and circatidal phenotypes inEurydice pulchra (Ep), the speckled sea-louse. Here we show that these drug inhibitors of CK1 also affect the phosphorylation of EpCLK and EpBMAL1 and disrupt EpCLK-BMAL1-mediated transcription in Drosophila S2 cells, revealing a potential link between the positive circadian regulators and circatidal behaviour. We therefore performed dsRNAi knockdown of Epbmal1as well as the major negative regulator inEurydice, Epcry2. Epcry2and Epbmal1knockdown disruptedEurydice’s circadian phenotypes as expected but in addition, circatidal behaviour was also sensitive to Epbmal1knockdown. Thus threeEurydicenegative circadian regulators, EpCRY2, in addition to EpPER and EpTIM, do not appear to be required for the expression of circatidal behaviour, in contrast to the positive regulatorEpBMAL1. We suggest a neurogenetic model whereby the positive circadian regulators BMAL1-CLK are shared between circadian and circatidal mechanisms inEurydicebut circatidal rhythms require a novel, as yet unknown negative regulator.
Back to the Future- Unleashing your cytometer’s spectral potential
Authors: Hall Christopher , Ibrahim Hanan , Thompson Sam , Hobson Philip S , Crofts Jo-Anne , Nobes Peter , Lim Steven , Burpee Tony , Walker Rachael V
Published: December 2022

With the recent growth in spectral flow cytometry many laboratories are investing in new spectral flow cytometers in order to maximise the information gathered about every cell. This study hypothesised that traditional cytometers already within many laboratories may be used as spectral cytometers and have shown using a range of different cytometers that data acquired may be unmixed after acquisition.
The influence of N-methylation on the ansamers of an amatoxin: Gly5Sar-amanullin
Authors: Wenz Marius T. , Kosol Simone , Yao Guiyang , Süssmuth Roderich D. , Keller Bettina G.
Published: December 2022

Amatoxins are strong inhibitors of RNA polymerase II, and cause cell death. Because of their cytotoxicity they are candidates for anti-cancer drugs, and understanding their structure-activity relationship is crucial. Amatoxins have a rigid bicyclic scaffold which consists of a cyclic octapeptide bridged by cysteine and tryptophan side chain forming a tryptathionine bridge. Here we show the influence of the N-methylation on the amatoxin scaffold by studying Gly5Sar-amanullin with MD simulations and NMR experiments. Since we have shown recently that the amatoxin scaffold allows for two isomeric forms (ansamers), we studied both isomers of Gly5Sar-amanullin. We found that both isomers of Gly5Sar-amanullin form two long-living conformations which is unusual for amatoxins, and that they are differently affected by the N-methylation. The natural Gly5Sar-amanullin forfeits the hydrogen bonds to Gly5 due to the N-methylation, which is expected from existing crystal structures for alpha-amanitin. Our results however indicate that this does not cause more flexibility due to a shift in the hydrogen bond pattern. In the unnatural isomer, we observe an interesting cis-trans-isomerisation of the backbone angles in Trp4 and Gly7, which is enabled by the N-methylation. We expect that our perspective on the effect of N-methylation in amatoxins could be a starting point for further SAR-studies which are urgently needed for the design of better anti-cancer agents.
Enhanced Viral Metagenomics with Lazypipe 2
Authors: Plyusnin Ilya , Vapalahti Olli , Sironen Tarja , Kant Ravi , Smura Teemu
Published: December 2022

Viruses are the main agents causing emerging and re-emerging infectious diseases. It is therefore important to screen for and detect them and uncover the evolutionary processes that support their ability to jump species boundaries and establish themselves in new hosts. Metagenomic next-generation sequencing (mNGS) is a high-throughput, impartial technology that has enabled virologists to detect either known or novel, divergent viruses from clinical, animal, wildlife and environmental samples, with little a priori assumptions. mNGS is heavily dependent on bioinformatic analysis, with an emerging demand for integrated bioinformatic workflows. Here, we present Lazypipe2, an updated mNGS pipeline with, as compared to Lazypipe1, significant improvements in code stability, transparency, with added functionality and support for new software components. We also present extensive benchmarking results, including evaluation on a novel canine simulated metagenome, and precision and recall of virus detection at varying sequencing depth and low to extremely low proportion of viral genetic material. Additionally we report accuracy of virus detection with two strategies: homology searches using nucleotide or amino acid sequences. We show that Lazypipe2 with nucleotide-based annotation approaches near perfect detection of eukaryotic viruses and, in terms of accuracy, outperforms the compared pipelines. We also discuss the importance of homology searches with amino acid sequences for the detection of highly divergent novel viruses.
Weight loss improves skeletal muscle mitochondrial energy efficiency
Authors: Ferrara Patrick J. , Lang Marisa J. , Johnson Jordan M. , Watanabe Shinya , McLaughlin Kelsey L. , Maschek J. Alan , Verkerke Anthony R.P. , Siripoksup Piyarat , Chaix Amandine , Cox James E. , Fisher-Wellman Kelsey H. , Funai Katsuhiko
Published: December 2022

Weight loss is associated with a disproportionate decrease in whole-body energy expenditure that may contribute to the heightened risk for weight-regain. Evidence suggests that this energetic mismatch originates from lean tissue. Although this phenomenon is well documented, the mechanisms have remained elusive. We hypothesized that increased mitochondrial energy efficiency in skeletal muscle is associated with reduced expenditure under weight loss. Wildtype male C57BL6/N mice were fed with high-fat diet for 10 wks, followed by a subset of mice that were maintained on the obesogenic diet (OB) or switched to standard chow to promote weight loss (WL) for additional 6 wks. Mitochondrial energy efficiency was evaluated using high-resolution respirometry and fluorometry. Mass spectrometric analyses were employed to describe the mitochondrial proteome and lipidome. Weight loss promoted ~50% increase in the efficiency of oxidative phosphorylation (ATP produced per O2consumed, or P/O) in skeletal muscle. However, weight loss did not appear to induce significant changes in mitochondrial proteome, nor any changes in respiratory supercomplex formation. Instead, it accelerated the remodeling of mitochondrial cardiolipin (CL) acyl-chains to increase tetralinoleoyl CL (TLCL) content, a species of lipids thought to be functionally critical for the respiratory enzymes. We further show that lowering TLCL by deleting the CL transacylase tafazzin was sufficient to reduce skeletal muscle P/O and protect mice from diet-induced weight gain. These findings implicate skeletal muscle mitochondrial efficiency as a novel mechanism by which weight loss reduces energy expenditure in obesity.