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Stem cells isolated from amniotic fluid are known to be able to differentiate into different cells types, thus being considered as a powerful tool for cellular therapy of different human diseases. In the last 4 years, amniotic fluid-derived stem (AFS) cells have been shown to express embryonic and adult stem cell markers. These cells can be considered an intermediate stage between embryonic stem cells and adult stem cells. AFS cells can give rise to adipogenic, osteogenic, myogenic, endothelial, neurogenic, and hepatic lineages, inclusive of all embryonic germ layers. AFS cells have a high renewal capacity and can be expanded for over 250 doublings without any detectable loss of chromosomal telomere length. Taken together, all these data provide evidence that amniotic fluid represents a new and very promising source of stem cells for research, as well as clinical applications. Certainly stem cells from amniotic fluid will be useful both for a customized cell supply for newly born children and for banking cells to be used for therapeutic cell transplantation in immunogically matched recipients. Further investigations are also warranted to fully explore the amniotic cells' potential for adult human disorders.

Community detection is a classic network problem with extensive applications in various fields. Its most common method is using modularity maximization heuristics which rarely return an optimal partition or anything similar. Partitions with globally optimal modularity are difficult to compute, and therefore have been underexplored. Using structurally diverse networks, we compare 30 community detection methods including our proposed algorithm that offers optimality and approximation guarantees: the Bayan algorithm. Unlike existing methods, Bayan globally maximizes modularity or approximates it within a factor. Our results show the distinctive accuracy and stability of maximum-modularity partitions in retrieving planted partitions at rates higher than most alternatives for a wide range of parameter settings in two standard benchmarks. Compared to the partitions from 29 other algorithms, maximum-modularity partitions have the best medians for description length, coverage, performance, average conductance, and well clusteredness. These advantages come at the cost of additional computations which Bayan makes possible for small networks (networks that have up to 3000 edges in their largest connected component). Bayan is several times faster than using open-source and commercial solvers for modularity maximization, making it capable of finding optimal partitions for instances that cannot be optimized by any other existing method. Our results point to a few well-performing algorithms, among which Bayan stands out as the most reliable method for small networks. A python implementation of the Bayan algorithm (bayanpy) is publicly available through the package installer for python.

Elevated osteoclast (OC)-mediated bone resorption, a common pathological feature between periodontitis and rheumatoid arthritis (RA), implicates a possible mutually shared pathogenesis. The autoantibody to citrullinated vimentin (CV), a representative biomarker of RA, is reported to promote osteoclastogenesis (OC-genesis). However, its effect on OC-genesis in the context of periodontitis remains to be elucidated. In an in vitro experiment, the addition of exogenous CV upregulated the development of Tartrate-resistant acid phosphatase (TRAP)-positive multinuclear OCs from mouse bone marrow cells and increased the formation of resorption pits. However, Cl-amidine, an irreversible pan-peptidyl arginine deiminase (PAD) inhibitor, suppressed the production and secretion of CV from RANKL-stimulated OC precursors, suggesting that the citrullination of vimentin occurs in OC precursors. On the other hand, the anti-vimentin neutralizing antibody suppressed in vitro Receptor activator of nuclear factor kappa-Β ligand (RANKL)-induced OC-genesis. The CV-induced upregulation of OC-genesis was abrogated by the Protein kinase C (PKC)-δ inhibitor Rottlerin, accompanied by the downmodulation of OC-genesis-related genes, including Osteoclast stimulatory transmembrane protein (OC-STAMP), TRAP and Matrix Metallopeptidase 9 (MMP9) as well as extracellular signal-regulated kinase (ERK) mitogen-activated protein (MAP)-kinase phosphorylation. Elevated levels of soluble CV and vimentin-bearing mononuclear cells were found in the bone resorption lesions of periodontitis induced in mice in the absence of an anti-CV antibody. Finally, local injection of anti-vimentin neutralizing antibody suppressed the periodontal bone loss induced in mice. Collectively, these results indicated that the extracellular release of CV promoted OC-genesis and bone resorption in periodontitis.

Background: To tackle the missing heritability of sporadic heart failure, we screened for novel heart failure-associated genetic variants in the Finnish population and functionally characterized a novel variant in vitro and in vivo., Methods and Results: Heart failure-associated variants were screened in genotyping array data of the FINRISK study, consisting of 994 cases and 20,118 controls. Based on logistic regression analysis, a potentially damaging variant in TRIM55 (rs138811034), encoding an E140K variant, was selected for validations. In HL-1 cardiomyocytes, we used CRISPR/Cas9 technology to introduce the variant in the endogenous locus, and additionally TRIM55 wildtype or E140K was overexpressed from plasmid. Functional responses were profiled using whole-genome RNA sequencing, RT-PCR and Western analyses, cell viability and cell cycle assays and cell surface area measurements. In zebrafish embryos, cardiac contractility was measured using videomicroscopy after CRISPR-mediated knockout of trim55a or plasmid overexpression of TRIM55 WT or E140K. Genes related to muscle contraction and cardiac stress were highly regulated in Trim55 E140K/- cardiomyocytes. When compared to the WT/WT cells, the variant cells demonstrated reduced viability, significant hypertrophic response to isoproterenol, p21 protein overexpression and impaired cell cycle progression. In zebrafish embryos, the deletion of trim55a or overexpression of TRIM55 E140K reduced cardiac contractility as compared to embryos with wildtype genotype or overexpression of WT TRIM55, respectively., Conclusions: A previously uncharacterized TRIM55 E140K variant demonstrated a number of functional implications for cardiomyocyte functions in vitro and in vivo. These findings suggest a novel role for TRIM55 polymorphism in predisposing to heart failure., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Increasing evidence suggests that the immune system affects prognosis of chronic myeloid leukemia (CML), but the detailed immunological composition of the leukemia bone marrow (BM) microenvironment is unknown. We aimed to characterize the immune landscape of the CML BM and predict the current treatment goal of tyrosine kinase inhibitor (TKI) therapy, molecular remission 4.0 (MR4.0). Using multiplex immunohistochemistry (mIHC) and automated image analysis, we studied BM tissues of CML patients (n = 56) and controls (n = 14) with a total of 30 immunophenotype markers essential in cancer immunology. CML patients' CD4+ and CD8+ T-cells expressed higher levels of putative exhaustion markers PD1, TIM3, and CTLA4 when compared to control. PD1 expression was higher in BM compared to paired peripheral blood (PB) samples, and decreased during TKI therapy. By combining clinical parameters and immune profiles, low CD4+ T-cell proportion, high proportion of PD1+TIM3-CD8+ T cells, and high PB neutrophil count were most predictive of lower MR4.0 likelihood. Low CD4+ T-cell proportion and high PB neutrophil counts predicted MR4.0 also in a validation cohort (n = 52) analyzed with flow cytometry. In summary, the CML BM is characterized by immune suppression and immune biomarkers predicted MR4.0, thus warranting further testing of immunomodulatory drugs in CML treatment.

To characterize type 2 diabetes (T2D)-associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D case and 132,532 control subjects of European ancestry after imputation using the 1000 Genomes multiethnic reference panel. Promising association signals were followed up in additional data sets (of 14,545 or 7,397 T2D case and 38,994 or 71,604 control subjects). We identified 13 novel T2D-associated loci ( P < 5 × 10 -8 ), including variants near the GLP2R , GIP , and HLA-DQA1 genes. Our analysis brought the total number of independent T2D associations to 128 distinct signals at 113 loci. Despite substantially increased sample size and more complete coverage of low-frequency variation, all novel associations were driven by common single nucleotide variants. Credible sets of potentially causal variants were generally larger than those based on imputation with earlier reference panels, consistent with resolution of causal signals to common risk haplotypes. Stratification of T2D-associated loci based on T2D-related quantitative trait associations revealed tissue-specific enrichment of regulatory annotations in pancreatic islet enhancers for loci influencing insulin secretion and in adipocytes, monocytes, and hepatocytes for insulin action-associated loci. These findings highlight the predominant role played by common variants of modest effect and the diversity of biological mechanisms influencing T2D pathophysiology., (© 2017 by the American Diabetes Association.)

The genetic features of isolated populations can boost power in complex-trait association studies, and an in-depth understanding of how their genetic variation has been shaped by their demographic history can help leverage these advantageous characteristics. Here, we perform a comprehensive investigation using 3,059 newly generated low-depth whole-genome sequences from eight European isolates and two matched general populations, together with published data from the 1000 Genomes Project and UK10K. Sequencing data give deeper and richer insights into population demography and genetic characteristics than genotype-chip data, distinguishing related populations more effectively and allowing their functional variants to be studied more fully. We demonstrate relaxation of purifying selection in the isolates, leading to enrichment of rare and low-frequency functional variants, using novel statistics, DVxy and SVxy. We also develop an isolation-index (Isx) that predicts the overall level of such key genetic characteristics and can thus help guide population choice in future complex-trait association studies.

Isolated populations with enrichment of variants due to recent population bottlenecks provide a powerful resource for identifying disease-associated genetic variants and genes. As a model of an isolate population, we sequenced the genomes of 1463 Finnish individuals as part of the Sequencing Initiative Suomi (SISu) Project. We compared the genomic profiles of the 1463 Finns to a sample of 1463 British individuals that were sequenced in parallel as part of the UK10K Project. Whereas there were no major differences in the allele frequency of common variants, a significant depletion of variants in the rare frequency spectrum was observed in Finns when comparing the two populations. On the other hand, we observed >2.1 million variants that were twice as frequent among Finns compared with Britons and 800 000 variants that were more than 10 times more frequent in Finns. Furthermore, in Finns we observed a relative proportional enrichment of variants in the minor allele frequency range between 2 and 5% (P<2.2 × 10 -16 ). When stratified by their functional annotations, loss-of-function variants showed the highest proportional enrichment in Finns (P=0.0291). In the non-coding part of the genome, variants in conserved regions (P=0.002) and promoters (P=0.01) were also significantly enriched in the Finnish samples. These functional categories represent the highest a priori power for downstream association studies of rare variants using population isolates.

Rheumatoid arthritis (RA) affects millions world-wide. While anti-TNF treatment is widely used to reduce disease progression, treatment fails in ∼one-third of patients. No biomarker currently exists that identifies non-responders before treatment. A rigorous community-based assessment of the utility of SNP data for predicting anti-TNF treatment efficacy in RA patients was performed in the context of a DREAM Challenge (http://www.synapse.org/RA&#95;Challenge). An open challenge framework enabled the comparative evaluation of predictions developed by 73 research groups using the most comprehensive available data and covering a wide range of state-of-the-art modelling methodologies. Despite a significant genetic heritability estimate of treatment non-response trait (h(2)=0.18, P value=0.02), no significant genetic contribution to prediction accuracy is observed. Results formally confirm the expectations of the rheumatology community that SNP information does not significantly improve predictive performance relative to standard clinical traits, thereby justifying a refocusing of future efforts on collection of other data.

By analyzing the whole-exome sequences of 4,264 schizophrenia cases, 9,343 controls and 1,077 trios, we identified a genome-wide significant association between rare loss-of-function (LoF) variants in SETD1A and risk for schizophrenia (P = 3.3 × 10(-9)). We found only two heterozygous LoF variants in 45,376 exomes from individuals without a neuropsychiatric diagnosis, indicating that SETD1A is substantially depleted of LoF variants in the general population. Seven of the ten individuals with schizophrenia carrying SETD1A LoF variants also had learning difficulties. We further identified four SETD1A LoF carriers among 4,281 children with severe developmental disorders and two more carriers in an independent sample of 5,720 Finnish exomes, both with notable neuropsychiatric phenotypes. Together, our observations indicate that LoF variants in SETD1A cause a range of neurodevelopmental disorders, including schizophrenia. Combining these data with previous common variant evidence, we suggest that epigenetic dysregulation, specifically in the histone H3K4 methylation pathway, is an important mechanism in the pathogenesis of schizophrenia.

We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease.

Constitutional delay of growth and puberty (CDGP) is the most common cause of pubertal delay. CDGP is defined as the proportion of the normal population who experience pubertal onset at least 2 SD later than the population mean, representing 2.3% of all adolescents. While adolescents with CDGP spontaneously enter puberty, they are at risk for short stature, decreased bone mineral density, and psychosocial problems. Genetic factors contribute heavily to the timing of puberty, but the vast majority of CDGP cases remain biologically unexplained, and there is no definitive test to distinguish CDGP from pathological absence of puberty during adolescence. Recently, we published a study identifying significant linkage between a locus at the pericentromeric region of chromosome 2 (chr 2) and CDGP in Finnish families. To investigate this region for causal variation, we sequenced chr 2 between the genomic coordinates of 79-124 Mb (genome build GRCh37) in the proband and affected parent of the 13 families contributing most to this linkage signal. One gene, DNAH6, harbored 6 protein-altering low-frequency variants (< 6% in the Finnish population) in 10 of the CDGP probands. We sequenced an additional 135 unrelated Finnish CDGP subjects and utilized the unique Sequencing Initiative Suomi (SISu) population reference exome set to show that while 5 of these variants were present in the CDGP set, they were also present in the Finnish population at similar frequencies. Additional variants in the targeted region could not be prioritized for follow-up, possibly due to gaps in sequencing coverage or lack of functional knowledge of non-genic genomic regions. Thus, despite having a well-characterized sample collection from a genetically homogeneous population with a large population-based reference sequence dataset, we were unable to pinpoint variation in the linked region predisposing delayed puberty. This study highlights the difficulties of detecting genetic variants under linkage regions for complex traits and suggests that advancements in annotation of gene function and regulatory regions of the genome will be critical for solving the genetic background of complex phenotypes like CDGP.

Background and Purpose: Besides the opportunities for reuse, stringent regulations and growing public awareness demand an enhanced quality of effluent from dye industries. Treatment of an aqueous solution of dye (reactive red 198) was carried out in a nanofiltration unit using both flat sheet and spiral wound modules to obtain a comparative performance evaluation in terms of permeate flux and quality., Methods: Hydrophilized polyamide membrane with molecular weight cutoff of 150 was used for the experiments. Effects of trans-membrane pressure (TMP), feed concentration and addition of salt on permeate flux were investigated. Percent reduction of color, chemical oxygen demand (COD), total dissolved solid (TDS), and conductivity were determined to assess performance of the membrane., Results: The maximum flux decline was 16.1% of its initial value at 490 kPa TMP with 50 ppm feed concentration in spiral wound module, whereas the same in flat sheet under same conditions was 7.2%. The effect of TMP showed a quasi-linear increase in flux with increasing pressure. Increased permeate concentration led to the reduction in observed retention of dye in the membrane. The average reduction in color, COD, and TDS were 96.88%, 97.38%, and 89.24%, respectively. The decline in permeate flux was more in case of spiral wound module compared to flat sheet. However, spiral wound module performed better in terms of color removal, COD reduction, and TDS removal., Conclusion: Substantial removal of color was achieved in the nanofiltration experiments with a marked reduction in COD and TDS. The process allowed the production of permeate stream with great reutilization possibilities.

This prospective randomized trial was undertaken to determine the added efficacy of (32)P in treating locally advanced unresectable pancreatic cancer. Thirty patients with biopsy proven locally advanced unresectable adenocarcinoma of the pancreas were assessable after receiving 5-fluorouracil and radiation therapy with or without (32)P, followed by gemcitabine. Intratumoral (32)P dose was determined by tumor size and volume and was administered at months 0, 1, 2, 6, 7, and 8. Tumor cross-sectional area and liquefaction were determined at intervals by computed tomography scan. Tumor liquefaction occurred in 78% of patients receiving (32)P and in 8% of patients not receiving (32)P, although tumor cross-sectional area did not decrease. Serious adverse events occurred more often per patient for patients receiving (32)P (4.2 +/- 3.1 vs. 1.8 +/- 1.9; p = 0.03) leading to more hospitalizations. Death was because of disease progression (23 patients), gastrointenstinal hemorrhage (4 patients), and stroke (1 patient). One patient not receiving (32)P and one receiving (32)P are alive at 28 and 13 months, respectively. (32)P did not prolong survival (7.4 +/- 5.5 months with (32)P vs. 11.5 +/- 8.0 months without (32)P, p = 0.16). (32)P promoted tumor liquefaction, but did not decrease tumor size. Intratumoral (32)P was associated with more serious adverse events and did not improve survival for locally advanced unresectable pancreatic cancer.

Objective: To demonstrate that the positive parathyroid sestamibi scan, if correctly interpreted and applied, truly represents a parathyroid adenoma, never a "false-positive" scan., Summary Background Data: Although the sestamibi scan is widely ordered preoperatively to locate parathyroid adenomas, concern about a false-positive scan often causes surgeons to distrust the results. Tissues such as thyroid adenomas and lymph nodes have been blamed for false-positive studies, but the radioactivity of these presumed false-positive tissues has never been measured., Methods: Over an 1 8-month period, 17 patients were referred for persistent primary hyperparathyroidism after undergoing at least one neck exploration. All patients had a sestamibi scan prior to their initial operation that was interpreted as clearly positive and then, during or after an unsuccessful operation, deemed false-positive by the surgeon. At the authors' institution, all patients underwent repeat sestamibi scintigraphy and were taken to the operating room while radioactive for a minimally invasive radioguided parathyroidectomy (MIRP)., Results: The authors' sestamibi scans demonstrated the same single focus of radioactivity displayed on the outside scans, clearly positive. During MIRP, an adenoma was successfully located and removed in all patients, with confirmation of the diagnosis by quantitative differential radioactivity and subsequent histologic examination. Removal of the radioactive tissue cured all patients., Conclusion: Intraoperative nuclear mapping permitted identification and removal of parathyroid adenomas in all patients with positive sestamibi scans that had previously been labelled false-positive, indicating that each patient would have been cured during their previous operation if radioguided techniques were used. Surgeons should be extremely cautious in deciding intraoperatively that a positive sestamibi scan is a false-positive scan.

Purpose: We evaluated the difference in response patterns of captopril versus standard renography for assessing hydronephrosis due to suspected ureteropelvic and ureterovesical junction obstruction. This technique may identify hydronephrotic kidneys in which normal function is maintained by vasoactive compensatory mechanisms. Sustained obstruction may cause these mechanisms to fail, and expose the kidneys to permanent functional deterioration in the long term., Material and Methods: We prospectively studied 15 boys and 8 girls with a mean age of 3.5 years with grades III to IV/IV hydronephrosis. Evaluations included renal sonography, standard diuretic and captopril renography, glomerular filtration rate, voiding cystography, serum creatinine, blood pressure, and urinalysis with culture and sensitivity. Obstruction was suspected at the ureteropelvic junction in 19 kidneys and at the ureterovesical junction in 9. We compared differential function values obtained by standard diuretic and captopril renography., Results: We observed certain patterns in response to captopril renography, including pattern 1--unilateral decrease in hydronephrotic kidney relative function in 5 of 23 cases, 2--bilateral decreased function in 2, 3--bilateral increased function in 4 and 4--no change in function in 12 on standard renography. When half-time was more than 20 minutes on standard diuretic renography in 8 cases, captopril renography showed an ipsilateral decrease and bilateral increase in glomerular filtration rate in 4 and 1, respectively, and no change in 3. In 12 of the 23 patients (52%) there was no difference in the results of captopril and diuretic renography as well as no change in differential function on standard diuretic renography during 1 1/2 years of observation. Surgical correction was performed in 4 patients in whom half-time was greater than 20 minutes and differential function was decreased on captopril renography., Conclusions: Our preliminary study reveals that there may be a role for captopril renography for detecting renin-angiotensin system mediated compensatory mechanisms in obstructive uropathy. When such compensatory mechanisms are activated, they may be unmasked by captopril, producing 1 of 4 patterns on renography and glomerular filtration rate. Patterns may indicate different degrees of impending renal function impairment and, thus, they may become useful for determining the progression of injury, when present, and the appropriate timing of surgical intervention.

Primarily because of the lack of highly accurate preoperative localizing studies, the standard operation for primary hyperparathyroidism (HPTH) has consisted of bilateral neck exploration with examination of all four parathyroid glands. Recent experience with the technetium-99m-Sestamibi scan at our hospital has suggested that this single test was now accurate enough to allow unilateral neck exploration. This study was designed to examine the efficacy and safety of minimally invasive parathyroid-ectomy in select patients with a single adenoma demonstrated on a preoperative sestamibi. Eighteen consecutive patients with primary HPTH in whom a sestamibi scan suggested a single adenoma underwent unilateral neck exploration through a 2.5-cm incision, which was extended as necessary. Results were compared to the preceding 25 parathyroid explorations for primary HPTH due to a single adenoma, which were nondirected and included bilateral neck exploration. All patients undergoing minimal exploration were found to have a single adenoma and demonstrated a normal serum calcium within 24 hours of surgery. Standard bilateral exploration failed to locate the adenoma in one patient requiring subsequent re-exploration. Operative time, incision length, and length of hospital stay were all significantly less for those undergoing minimal exploration (all P < 0.01). There were no complications in either group. Minimally invasive neck exploration is a safe and effective treatment for primary HPTH, is easily accomplished under local anesthesia, and is associated with significant reductions in operative time and hospital stay. Limited exploration provides a better cosmetic result while decreasing the potential complications of bilateral exploration, but is dependent upon a high-quality sestamibi scan.

Background: The inability to predict the location and number of diseased parathyroid glands has precluded the wide acceptance of unilateral neck exploration for primary hyperparathyroidism. We used intraoperative nuclear mapping in patients identified by sestamibi scanning to have a single adenoma in hopes of minimizing operative intervention while maintaining the efficacy of a full exploration., Methods: Fifteen consecutive patients with primary hyperparathyroidism underwent technetium 99m-labeled sestamibi scanning 3.0 +/- 0.1 hours before operation. Placement of the initial 2.0 cm incision and all dissection were guided by quantitative gamma counting in four neck quadrants with an 11 mm Neoprobe. Ex vivo radioactivity was determined for parathyroid glands, fat, and lymph nodes. Potential radiation hazards were assessed., Results: Intraoperative nuclear mapping discriminated between 14 solitary adenomas and one patient with four-gland hyperplasia that was not predicted on preoperative sestamibi scanning. Removal of the adenoma resulted in a decline in radioactivity in that quadrant (p < 0.001) and the entire neck (p < 0.05), with equalization of all neck quadrants. Ex vivo counts always identified parathyroid tissue (p < 0.0001 versus fat and lymph node). Adenomas were located in 19 +/- 1.7 minutes through a 2.3 +/- 0.1 cm incision. No significant radiation hazard existed, and no special handling of the specimen was required (0.06 +/- 0.01 mR/hr)., Conclusions: Intraoperative nuclear mapping complements sestamibi scanning to help distinguish single-gland from multigland disease. This technique allows for a minimally invasive operation under local anesthesia in a true outpatient setting.

Sodium pertechnetate Tc99m scintigraphy is a valuable technique for the evaluation of acute testicular torsion in postpubescent males. However, in neonates and children with small testicles, the method is less reliable. Since the testicles of adult rats and young children are of similar size, the reliability of testicular imaging for detecting torsion was evaluated in this species. The utility of the radionuclide angiogram (RA) and static images were determined in 17 anesthetized animals before, 2 h after and 20 h after ligation of the left spermatic cord. The preligation RA was asymmetric in 27% of animals, while the static images were abnormal in 18%. Postligation flow and static images were abnormal in 57% and 82% of the animals (localized to the correct side, 38% and 36%), respectively. The animals with vascular occlusion failed to show any statistically significant greater incidence of decreased radionuclide accumulation on the ligated side. To determine the influence of relative perfusion and extracellular fluid space of the scrotum and testicles on the images, additional studies were performed with 201Tl (representing perfusion) and 99mTcO4- (representing ECF space). Perfusion was approximately equal in the testis and epididymis but significantly higher in the scrotum. These results suggest that scrotal scintigraphy is unreliable for detecting acute torsion of small testicles.