Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA-Binding Protein HuR Regulates Paneth Cell Function by Altering Membrane Localization of TLR2 via Posttranscriptional Control of CNPY3.

BACKGROUND & AIMS Paneth cells secrete antimicrobial proteins including lysozyme via secretory autophagy as part of the mucosal protective response. The ELAV like RNA-binding protein 1 (ELAVL1, also called HuR) regulates stability and translation of mRNAs and many aspects of mucosal physiology. We studied the posttranscriptional mechanisms by which HuR regulates Paneth cell function. METHODS Intestinal mucosal tissues were collected from mice with intestinal epithelium-specific disruption of HuR (IE-HuR-/-), HuRfl/fl-Cre- mice (controls), and patients with inflammatory bowel diseases (IBD) and analyzed by histology and immunohistochemistry. Paneth cell functions were determined by lysozyme-immunostaining assays. We isolated primary enterocytes from IE-HuR-/- and control mice and derived intestinal organoids. HuR and the chaperone CNPY3 were overexpressed from transgenes in intestinal epithelial cells (IECs) or knocked down with small interfering RNAs. We performed RNA pulldown assays to investigate interactions between HuR and its target mRNAs. RESULTS Intestinal tissues from IE-HuR-/- mice had reduced numbers of Paneth cells, and Paneth cells had fewer lysozyme granules per cell, compared with tissues from control mice, but there were no effects on goblet cells or enterocytes. Intestinal mucosa from patients with IBD had reduced levels of HuR and fewer Paneth cells. IE-HuR-/- mice did not have the apical distribution of TLR2 in the intestinal mucosa as observed in control mice. IECs from IE-HuR-/- mice expressed lower levels of CNPY3. Intestinal organoids from IE-HuR-/- mice were smaller and contained fewer buds compared with those generated from controls, and had fewer lysozyme-positive cells. In IECs, knockdown of HuR decreased levels of the autophagy proteins LC3-I and LC3-II, compared with control cells, and prevented rapamycin-induced autophagy. We found HuR to interact directly with the Cnpy3 mRNA coding region and increase levels of CNPY3 by increasing the stability and translation of Cnpy3 mRNA. CNPY3 bound TLR2, and cells with knockdown of CNPY3 or HuR lost membrane localization of TLR2, but increased cytoplasmic levels of TLR2. CONCLUSIONS In studies of mice, IECs, and human tissues, we found HuR to increase expression of CNPY3 at the posttranscriptional level. CNPY3 is required for membrane localization of TLR2 and Paneth cell function.
What comorbidities accompany sarcoidosis? A large cohort (n=1779) patients analysis.

BACKGROUND Sarcoidosis is a systemic granulomatous multiorgan disease with the most common manifestation is in the chest, although the granulomas can also involve all other organs causing variety of symptoms mimicking different diseases. OBJECTIVES To evaluate the incidence of comorbidity in a large group of patients with sarcoidosis diagnosed or followed in referral center for lung diseases in Poland. PATIENTS AND METHODS We performed a retrospective analysis in a group of 1779 patients discharged with the final diagnosis "sarcoidosis" (ICD-10: D86) from January 2008 to October 2011. RESULTS The majority (79.2%) were diagnosed as pulmonary and/or lymph node sarcoidosis (D86.0, D86.1, D86.2). Sarcoidosis of other and combined sites (D86.8) were diagnosed in 15.8% and unspecified (D86.9) in 5.0% of patients. At least one comorbid condition was noted in 54% of the patients, most frequently arterial hypertension (22.4%), thyroid disorders (5.6%), diabetes mellitus (5.0%), COPD (4.3%) and obesity (3.3%). Using linear regression models, the associations between the number of comorbidities and age and extent of the disease were found (p<0.001). Patients with multiorgan sarcoidosis were more likely to have a comorbid condition. CONCLUSIONS More than half of patients with sarcoidosis have a comorbid condition, which is more likely in older patients and those with multiorgan involvement.
Small‐fiber sensory neuropathies: Clinical course and neuropathology of idiopathic cases

We describe the clinical features, natural history, and neuropathology of 32 patients presenting with “burning feet”, for whom no specific cause was identified. All had neuropathic pain in the feet and morphological abnormalities of cutaneous innervation in skin obtained using punch biopsy. Most (29) had an abnormal sensory examination. All had normal strength, proprioception, tendon reflexes, and nerve conductions. Two clinical patterns were apparent, based on natural history and spatial distribution of cutaneous denervation. Most (28) patients presented with neuropathic pain initially restricted to the feet and toes but extending more proximally to involve the legs and hands with time. Intraepidermal nerve fiber (IENF) density was most severely reduced distally, with more normal IENF densities in skin from proximal sites. In contrast, a minority (4) presented with the abrupt onset of generalized cutaneous burning pain and hyperesthesia. In these patients, IENF densities were reduced in skin from both proximal and distal sites. Absolute IENF densities in calf skin were reduced below the lower limit of normal (5th percentile) in 26 (81%). Of the 6 who underwent sural nerve biopsy, 4 had selective loss of small myelinated and/or unmyelinated axons and 2 had normal histology and fiber densities despite reduced IENF densities in skin biopsy specimens. Punch skin biopsy from proximal and distal sites is a useful means of assessing these distinctive patients and may provide further insight into pathophysiology.
Opposing effects of IL-1β/COX-2/PGE2 pathway loop on islets in type 2 diabetes mellitus.

The cyclooxygenase2 (COX-2) enzyme catalyzes the first step of prostanoid biosynthesis, and is known for its crucial role in the pathogenesis of several inflammatory diseases including Type 2 Diabetes Mellitus (T2DM). Although a variety of studies revealed that COX-2 played a role in the IL-1β induced β cell dysfunction, the molecular mechanism remains unclear. Here, using a cDNA microarray and in silico analysis, we demonstrated that inflammatory responses were upregulated in human T2DM islets compared with non-diabetic (ND) islets. COX-2 expression was significantly enhanced in human T2DM islets, correlated with the high inflammation level. PGE2, the catalytic product of COX-2, downregulated the functional gene expression of PDX1, NKX6.1, and MAFA and blunted the glucose induced insulin secretion of human islets. Conversely, inhibition of COX-2 activity by a pharmaceutical inhibitor prevented the β-cell dysfunction induced by IL-1β. COX-2 inhibitor also abrogated the IL-1β autostimulation in β cells, which further resulted in reduced COX-2 expression in β cells. Together, our results revealed that COX-2/PGE2 signaling was involved in the regulation of IL-1β autostimulation, thus forming an IL-1β/COX-2/PGE2 pathway loop, which may result in the high inflammation level in human T2DM islets and the inflammatory impairment of β cells. Breaking this IL-1β/COX-2/PGE2 pathway loop provides a potential therapeutic strategy to improve β cell function in the treatment of T2DM patients.
Response by Smith and Gupta to Letter Regarding Article, "Computed Tomography Angiography Versus Digital Subtraction Angiography for Postclipping Aneurysm Obliteration Detection: A Meta-Analysis".

In Response: We thank Malhotra and Wu for their constructive comments regarding our study on the role of CTA versus DSA for postclipping aneurysm obliteration detection. Based on our meta-analysis of 13 studies and 510 patients, we calculated a pooled negative likelihood ratio of 0.31 (95% CI, 0.20–0.48), so we determined that CTA should not be the preferred modality to rule out residual aneurysms after clipping until further study. We agree with Malhotra and Wu that the studies included in this meta-analysis suggest that the residual aneurysms that were not detected by CTA, but were detected by DSA, were generally small remnants with unknown clinical significance. Our intent in this article is not to label CTA is a poor modality for detecting clinically actionable residual aneurysms. Rather, we believe that in comparison with DSA, CTA does perform poorly in visualizing all remnant aneurysms after clipping, which our study was primarily designed to determine. Our study design treated each missed aneurysm with equal weight, regardless of size. Malhotra and Wu raise the concern that the missed aneurysms on CTA may not be of clinical significance. Prior cohort studies have demonstrated that some residual aneurysms 1 to 2 mm in size have the potential to grow and rupture, though the problem remains that the long-term rate of growth and of retreatment for small remnants is unknown which limits the ability to weigh the short-term risks of DSA against the long-term harms of missing a small residual aneurysm. Further, surgeons may not know whether a residual exists and if so, its size, before postoperative imaging, which may hamper stratification of imaging choice based on size. Until the long-term behavior of these small remnants is better understood, DSA should remain the gold standard for imaging in this scenario. The presence of multiple clips may limit the performance of CTA because of artifact and believe that DSA will likely remain the appropriate modality for these patients. A better understanding of the variable behavior of remnant aneurysms after clipping may help establish which patients, if any, could be better served with CTA for remnant visualization. For example, age under 45 years has been identified as a risk factor for aneurysm remnant growth and could help stratify the postclipping imaging frequency and modality. As we begin to appreciate more about the significance of aneurysm remnants and as the technology of CTA improves, further stratification efforts may be possible; but based on the results of this meta-analysis, DSA continues to outperform CTA for detection of postclipping residuals. We recognize and thank Malhotra and Wu for their nuanced assessment of our study and contributions to this discussion.
Clinical Utility of a Risk‐Adapted Protocol for the Evaluation of Coronary Artery Disease in Liver Transplant Recipients

The prevalence and management of coronary artery disease (CAD) in liver transplantation (LT) candidates are not well characterized. The aims of this study were to evaluate the impact on clinical outcomes of a specifically designed protocol for the management of asymptomatic CAD in LT candidates and to investigate noninvasive risk profiles for obstructive and nonobstructive CAD for 202 LT candidates. Those with high baseline cardiovascular risk (CVR; defined by the presence of classic CVR factors and/or decreased ejection fraction) received coronary angiography and significant arterial stenosis and were treated with percutaneous stents. Patients were followed up after LT until death or coronary event (CE). There were 78 patients who received coronary evaluation (62 direct angiography, 14 computed tomography coronary angiography, and 2 both). Of them, 39 (50%) patients had CAD of any severity, and 6 (7.7%) had significant lesions (5 were amenable to be treated with stents, whereas 1 patient had diffuse lesions which contraindicated the LT). Insulin‐dependent diabetes was the only factor related to CAD of any severity (odds ratio, 3.44; 95% confidence interval [CI], 1.00‐11.97). A total of 69 patients (46 with coronary evaluation) received LT. The incidence of CEs and overall survival after LT were similar between patients with and without coronary evaluation. Furthermore, no differences occurred between these groups in a multivariate competing risk model (subhazard ratio, 0.84; 95% CI, 0.27‐2.61; P = 0.76). In conclusion, the application of an angiographic screening protocol of CAD in a selected high‐risk Mediterranean population is safe and effective. The short‐ and medium‐term incidence rates of CEs and death after LT in this population are similar to that observed in low‐risk patients.
Differential role of CD133 and CXCR4 in renal cell carcinoma

The chemokine receptor CXCR4 and CD133, putative stem cell markers, were previously described in renal cancer (RCC). To evaluate the biological and prognostic role of CD133 and CXCR4 in RCC the expression was evaluated through qPCR and immunoblotting in human renal cancer cell lines (786-O, A498, ACHN, CAKI-1, SN12C, TK10, UO31) and patients biopsies. Renal cancer cells and surgical biopsies expressed functional CXCR4 while CD133 was not detectable. CXCR4 and CD133 expression was then evaluated in 240 renal cancer patients through immunohistochemistry. CXCR4 and CD133 were low in 19.1% and 59.6%; intermediate in 20% and 17.9%; high in 60.8% and 22.5% of the cases, respectively. CXCR4 was overexpressed in tumours (p= 0.02), while CD133 was over expressed in healthy tissues (p= 0.04). Disease free survival Kaplan Meier plots suggest that prognosis is unfavourable for patients whose primary tumours express CXCR4 (p= 0.0199) but nor CD133 (p= 0.151) neither the concomitant CXCR4-CD133 (p=0.848) high expression affected prognosis. Analysis of prognostic factors suggests that age, clinical presentation, AJCC stage and CXCR4 had a significant prognostic value at the univariate analysis. The CXCR4 predictive ability was confirmed at the multivariate analysis while no prognostic role was identified for CD133. Thus concomitant CD133 and CXCR4 evaluation is not worth in RCC patient while the CXCR4 prognostic role encourage CXCR4 antagonists as promising therapeutic option.
Timing of Erythropoietin Treatment for Cardioprotection in Ischemia/Reperfusion

Erythropoietin (EPO) is a hormone known to stimulate hematopoiesis. However, recent research suggests additional properties of EPO, such as protection against ischemia/reperfusion (I/R) injury in various tissues. We studied the effect of timing of EPO administration on cardioprotection during I/R in the heart. Male Sprague–Dawley rats were subjected to 45 minutes of coronary occlusion, followed by 24 hours of reperfusion. Animals were randomized to receive saline or single dose of EPO (5000 IU/kg) either 2 hours before I/R, at the start of ischemia, or after the onset of reperfusion. The ratio of infarct area/area at risk (planimetry), left ventricular (LV) function (pressure development), and apoptosis (number of active caspase-3 positive cells) were determined after 24-hour reperfusion. Administration of EPO during different time points resulted in a 19 to 23% (P < 0.05) reduction in the infarct area/area at risk, which was accompanied by a trend toward better LV hemodynamic parameters. Apoptosis was significantly attenuated in groups treated with EPO at the start of ischemia (29% reduction) and after the onset of reperfusion (38%), and to a lesser extent (16%) in the group pre-treated with EPO. Thus, in vivo administration of EPO at different time points protects the myocardial structure and preserves cardiac function during I/R. Cardioprotective effect of EPO is associated with inhibition of apoptosis.
Effects of light quality on growth and quality of lettuces in hydroponic

The effects of light quality on growth and quality of lettuce in hydroponic were studied. There were 3 treatments: white LED as control (CK), white-red LED (R: W=1:4) (T1), red-white LED (R:W=1:1) (T2) (red LED light 660 ± 20 nm). The PAR (Photosynthetically Active Radiation) was 150 μ mol.m-2.s-1, irradiation duration: 6:30-18:30. The lettuces were grown 35 days under different light treatment. The results showed that the growth and quality of lettuce were significantly affected by light quality treatment. The growth of shoot and root in hydroponic lettuce were enhanced by red light, and increased with the ratio of red light increased. The fresh weight of shoot increased by 34.6% and 52.7%, and that of root by 46.9% and 97.8% in T1 and T2 treatment respectively. And the dry weight of shoot increased by 40.3% and 66.7%, and that of root by 62.5% and 91.7% in T1 and T2 treatment respectively. The contents of soluble sugar and Vitamin C increased under red light, and increased with the ratio of red light increased. The soluble sugar concentrations in lettuce increased by 19.8% and 94.7%, and Vitamin C concentration by 76.7% and 97.4% in T1 and T2 treatment respectively. The nitrate concentrations decreased under red light, and decreased with the ratio of red light increased. The nitrate concentrations in lettuce decreased by 37.8% and 40.1% in T1 and T2 treatment respectively. Thus more red light is benefit for the growth and quality of lettuce in hydroponic.
Enzymatic measurement of phosphatidylserine in cultured cells

Phosphatidylserine (PS) is a quantitatively minor membrane phospholipid involved in diverse cellular functions. In this study, we developed a new fluorometric method for measuring PS using combinations of specific enzymes and Amplex Red. The calibration curve for PS measurement was linear and hyperbolic at low (0–50 µM) and high (50–1000 µM) concentrations, respectively, and the detection limit was 5 µM (50 pmol in the reaction mixture). This assay quantified PS regardless of the chain length and the number of double bonds. We applied this new method to the determination of PS content in HEK293 cells, which was validated by a recovery study and comparison with TLC-phosphorus assay. We showed that the PS content was high in sparse cells. The overexpression of PS synthase 1 elevated not only the cellular PS content but also the phosphatidylcholine (PC) and phosphatidylethanolamine (PE) contents, suggesting the conversion of PS into PE and the enhancement of PC production. This new assay for PS measurement is simple, specific, sensitive, and high throughput, and it will be useful to clarify the metabolism and biological functions of PS.
Up-regulated expression of CXCL12 in human spleens with extramedullary haematopoiesis

Aims: To determine the expression of CXCL12 in human spleens with extramedullary haematopoiesis (EMH) for clarifying the association of splenic haematopoietic stem cells (HSCs) with CXCL12, which has been demonstrated to be a marker of bone marrow niches. Methods: We examined the expression of mRNA for CXCL12 by quantitative reverse transcription polymerase chain reaction (RT-PCR) and localised the CXCL12 protein by immunohistochemical staining in EMH negative and positive spleen samples from autopsy cases. Results: Expression of CXCL12 was significantly higher in samples from EMH positive cases than those from EMH negative cases. CXCL12 was localised to the endothelial cells of the sinuses of the red pulp in EMH positive spleens while vascular endothelial cells of the white pulp expressed CXCL12 throughout the spleen. c-kit positive/CD34 negative cells were identified in contact with CXCL12 positive endothelial cells of sinuses in EMH positive cases, although the number was few. In contrast, erythroblastic islands were frequently observed in EMH positive cases and dominantly localised to the intrasinusoidal spaces in association with CD68 positive macrophages. Conclusions: Our results suggest that endothelial cells of splenic sinuses expressing CXCL12 may contribute to attracting circulating haematopoietic precursor cells and constitute bone marrow niche-like regions of EMH in humans. Differentiating haematopoietic cells may move into intrasinusoidal spaces to form EMH foci such as erythroblastic accumulation.
Three-dimensional Monolayer Stress Microscopy

Many biological processes involve the collective generation and transmission of mechanical stresses across cell monolayers. In these processes, the monolayer undergoes lateral deformation and bending due to the tangential and normal components of the cell-generated stresses. Monolayer Stress Microscopy (MSM) methods have been developed to measure the intracellular stress distribution in cell monolayers. However, current methods assume plane monolayer geometry and neglect the contribution of bending to the intracellular stresses. This work introduces a three-dimensional (3D) MSM method that calculates monolayer stress from measurements of the 3D traction stresses exerted by the cells on a flexible substrate. The calculation is carried out by imposing equilibrium of forces and moments in the monolayer, subject to external loads given by the 3D traction stresses. The equilibrium equations are solved numerically, and the algorithm is validated for synthetic loads with known analytical solutions. We present 3D-MSM measurements of monolayer stress in micropatterned islands of endothelial cells of different sizes and shapes. These data indicate that intracellular stresses caused by lateral deformation emerge collectively over long distances; they increase with the distance from the island edge until they reach a constant value that is independent of island size. On the other hand, bending-induced intracellular stresses are more concentrated spatially and remain confined to within 1-2 cell lengths of bending sites. The magnitude of these bending stresses is highest at the edges of the cell islands, where they can exceed the intracellular stresses caused by lateral deformations. Our data from non-patterned monolayers suggests that biomechanical perturbations far away from monolayer edges also cause significant localized alterations in bending tension. The localized effect of bending-induced stresses may be important in processes like cellular extravasation, which are accompanied by significant normal deflections of a cell monolayer (i.e. the endothelium), and which require localized changes in monolayer permeability.
Comparison of a 2.5% and a 4.25% Dextrose Peritoneal Equilibration Test

Background Ultrafiltration (UF) failure develops over time in some patients on peritoneal dialysis. The workup of UF failure can be difficult and the 4.25% peritoneal equilibration test (PET) has been suggested to be more useful than the 2.5% PET for the workup of UF failure. It is unknown how a 4.25% PET compares to a 2.5% PET in individual patients. Objectives To assess the differences in drain volumes and sodium sieving using a 4.25% PET compared to a 2.5% PET, and to determine whether peritoneal transport rates, in terms of dialysate-to-plasma (D/P) ratios, are comparable between the two. Design Pilot study with each patient serving as his or her own control. Setting Outpatient dialysis facility of Wake Forest University Baptist Medical Center. Patients 47 patients, all of whom had a 2.5% PET and a 4.25% PET performed within 1 week of each other. Outcome Measures Dialysate-to-plasma ratios of urea and creatinine, dialysate total protein, and dialysate glucose compared to time zero (D/D0) at 0, 2, and 4 hours. Four-hour drain volumes and sodium sieving at 2 hours were also measured. Results There was reproducibility between the 2.5% and 4.25% PET for D/P ratios of urea and creatinine and for dialysate total protein. There were expected differences in drain volume, sodium sieving, and D/D0 glucose between the two methods. Conclusions The use of a 4.25% PET may be more useful for the workup of UF failure because of the accentuation of drain volume and sodium sieving, while remaining useful for prescription management.
Development of interneurons with ipsilateral projections in embryonic rat spinal cord

Considerable progress has been made in recent years in identifying molecules with restricted expression in mammalian spinal cord at early developmental stages. However, the significance of the different expression patterns for most of these molecules is nuclear because so little is known about the development of various classes of spinal interneurons. Recently, we have characterized the development of rat spinal cord interneurons with an axon that crosses in the ventral commissure (Silos‐Santiago and Snider, J. Comp. Neurol., 325:514, 1992). In the current study, we describe the morphological development of ipsilaterally projecting spinal interneurons in laminae V–VIII of the thoracic spinal cord. These neurons were labelled by retrograde lateral diffusion of DiI after crystals were placed in various locations in the embryonic thoracic cord.