Leveraging Prior Knowledge to Recover Characteristic Immune Regulatory Motifs in Gulf War Illness.

Potentially linked to the basic physiology of stress response, Gulf War Illness (GWI) is a debilitating condition presenting with complex immune, endocrine and neurological symptoms. Here we interrogate the immune response to physiological stress by measuring 16 blood-borne immune markers at 8 time points before, during and after maximum exercise challenge in n = 12 GWI veterans and n = 11 healthy veteran controls deployed to the same theater. Immune markers were combined into functional sets and the dynamics of their joint expression described as classical rate equations. These empirical networks were further informed structurally by projection onto prior knowledge networks mined from the literature. Of the 49 literature-informed immune signaling interactions, 21 were found active in the combined exercise response data. However, only 4 signals were common to both subject groups while 7 were uniquely active in GWI and 10 uniquely active in healthy veterans. Feedforward mediation of IL-23 and IL-17 by IL-6 and IL-10 emerged as distinguishing control elements that were characteristically active in GWI versus healthy subjects. Simulated restructuring of the regulatory circuitry in GWI as a result of applying an IL-6 receptor antagonist in combination with either a Th1 (IL-2, IFNγ, and TNFα) or IL-23 receptor antagonist predicted a partial rescue of immune response elements previously associated with illness severity. Overall, results suggest that pharmacologically altering the topology of the immune response circuitry identified as active in GWI can inform on strategies that while not curative, may nonetheless deliver a reduction in symptom burden. A lasting and more complete remission in GWI may therefore require manipulation of a broader physiology, namely one that includes endocrine oversight of immune function.

Astrocyte-specific transcriptome analysis using the ALDH1L1 bacTRAP mouse reveals novel biomarkers of astrogliosis in response to neurotoxicity.

Neurotoxicology is hampered by the inability to predict regional and cellular targets of toxicant-induced damage. Evaluating astrogliosis overcomes this problem because reactive astrocytes highlight the location of toxicant-induced damage. While enhanced expression of glial fibrillary acidic protein is a hallmark of astrogliosis, few other biomarkers have been identified. However, bacterial artificial chromosome - translating ribosome affinity purification (bacTRAP) technology allows for characterization of the actively translating transcriptome of a particular cell type; use of this technology in aldehyde dehydrogenase 1 family member L1 (ALDH1L1) bacTRAP mice can identify genes selectively expressed in astrocytes. The aim of this study was to characterize additional biomarkers of neurotoxicity-induced astrogliosis using ALDH1L1 bacTRAP mice. The known dopaminergic neurotoxicant 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP; 12.5 mg/kg s.c.) was used to induce astrogliosis. Striatal tissue was obtained 12, 24, and 48 h following exposure for the isolation of actively translating RNA. Subsequently, MPTP-induced changes in this RNA pool were analyzed by microarray and 184 statistically significant, differentially expressed genes were identified. The dataset was interrogated by gene ontology, pathway, and co-expression network analyses, which identified novel genes, as well as those with known immune and inflammatory functions. Using these analyses, we were directed to several genes associated with reactive astrocytes. Of these, TIMP1 and miR-147 were identified as candidate biomarkers because of their robust increased expression following both MPTP and trimethyl tin exposures. Thus, we have demonstrated that bacTRAP can be used to identify new biomarkers of astrogliosis and aid in the characterization of astrocyte phenotypes induced by toxicant exposures. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* because it provided all relevant information to reproduce the study in the manuscript. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/. Cover Image for this issue: doi: 10.1111/jnc.14518.

A retrospective analysis of complications of laparoscopic left donor nephrectomy using the Kocak's modification of Clavien-Dindo system.

INTRODUCTION: Kocak described a modification of Clavien-Dindo classification system (CDCS) for reporting procedure-related complications in laparoscopic donor nephrectomy (LDN). We used the Kocak modification in grading and reporting the severity of complications in patients who underwent LDN and in evaluating various parameters that predict them. METHODS: In all, 1430 patients who underwent left LDN from 2000 to 2016 were included in this study. All data was retrospectively collected and analyzed for complications occurring in the postoperative period. All complications were classified according to the four grades of Kocak-modified CDCS. RESULTS: 124 patients (8.6%) suffered a total of 235 postoperative complications. Most of the complications were Grade I and Grade II (Grade I: 79.5% [n = 187] and Grade II 16.2% [n = 38]), 2.5% of the complications were Grade III (n = 6) and Kocak Grade IVa complications occurred in three patients. There was one death (Grade IVb: 0.4%, overall mortality rate: 0.06%). The incidence of complications was significantly greater for male patients, those with body mass index ≥25 kg/m2, and if the operating surgeon had ≤ 1 year of experience in performing LDN surgery. CONCLUSION: LDN is a safe procedure with low morbidity. The rate of complications is 8.6% and most of these complications are of low grade. The use of a standardized system for reporting the complications of LDN allows appropriate comparison between reported data.

Single-centre experience of retroperitoneoscopic approach in urology with tips to overcome the steep learning curve.

CONTEXT: The retroperitoneoscopic or retroperitoneal (RP) surgical approach has not become as popular as the transperitoneal (TP) one due to the steeper learning curve. AIMS: Our single-institution experience focuses on the feasibility, advantages and complications of retroperitoneoscopic surgeries (RS) performed over the past 10 years. Tips and tricks have been discussed to overcome the steep learning curve and these are emphasised. SETTINGS AND DESIGN: This study made a retrospective analysis of computerised hospital data of patients who underwent RP urological procedures from 2003 to 2013 at a tertiary care centre. PATIENTS AND METHODS: Between 2003 and 2013, 314 cases of RS were performed for various urological procedures. We analysed the operative time, peri-operative complications, time to return of bowel sound, length of hospital stay, and advantages and difficulties involved. Post-operative complications were stratified into five grades using modified Clavien classification (MCC). RESULTS: RS were successfully completed in 95.5% of patients, with 4% of the procedures electively performed by the combined approach (both RP and TP); 3.2% required open conversion and 1.3% were converted to the TP approach. The most common cause for conversion was bleeding. Mean hospital stay was 3.2 ± 1.2 days and the mean time for returning of bowel sounds was 16.5 ± 5.4 h. Of the patients, 1.4% required peri-operative blood transfusion. A total of 16 patients (5%) had post-operative complications and the majority were grades I and II as per MCC. The rates of intra-operative and post-operative complications depended on the difficulty of the procedure, but the complications diminished over the years with the increasing experience of surgeons. CONCLUSION: Retroperitoneoscopy has proven an excellent approach, with certain advantages. The tips and tricks that have been provided and emphasised should definitely help to minimise the steep learning curve.

Inferring Broad Regulatory Biology from Time Course Data: Have We Reached an Upper Bound under Constraints Typical of In Vivo Studies?

There is a growing appreciation for the network biology that regulates the coordinated expression of molecular and cellular markers however questions persist regarding the identifiability of these networks. Here we explore some of the issues relevant to recovering directed regulatory networks from time course data collected under experimental constraints typical of in vivo studies. NetSim simulations of sparsely connected biological networks were used to evaluate two simple feature selection techniques used in the construction of linear Ordinary Differential Equation (ODE) models, namely truncation of terms versus latent vector projection. Performance was compared with ODE-based Time Series Network Identification (TSNI) integral, and the information-theoretic Time-Delay ARACNE (TD-ARACNE). Projection-based techniques and TSNI integral outperformed truncation-based selection and TD-ARACNE on aggregate networks with edge densities of 10-30%, i.e. transcription factor, protein-protein cliques and immune signaling networks. All were more robust to noise than truncation-based feature selection. Performance was comparable on the in silico 10-node DREAM 3 network, a 5-node Yeast synthetic network designed for In vivo Reverse-engineering and Modeling Assessment (IRMA) and a 9-node human HeLa cell cycle network of similar size and edge density. Performance was more sensitive to the number of time courses than to sample frequency and extrapolated better to larger networks by grouping experiments. In all cases performance declined rapidly in larger networks with lower edge density. Limited recovery and high false positive rates obtained overall bring into question our ability to generate informative time course data rather than the design of any particular reverse engineering algorithm.

Predictors for recurrence after urethroplasty in pediatric and adolescent stricture urethra.

OBJECTIVE: This study aims at evaluating factors predicting recurrence of urethral stricture following urethroplasty in pediatric patients at a tertiary care center. PATIENTS AND METHODS: Fifty-two patients of up to 18 years of age, who underwent urethroplasty, were reviewed. Duration of symptoms, etiology, previous intervention, and site of stricture, surgical modality, stricture length, and spongiofibrosis at stricture site, recurrence, and ancillary procedures required were recorded. RESULTS: Forty-two (82.76%) patients (Group I) had recurrence-free course on follow-up. Of the 10 patients with recurrence (Group II), 9 had PTS and 1 had IS (p = 0.04). Most of the factors evaluated did not differ statistically between the groups; however, length of stricture (1.8 vs. 4.3 cm, p < 0.001) and degree of spongiofibrosis (61% vs. 90%, p = 0.003) were significantly different. Seven patients with recurrence were managed with single procedures, but three required multiple procedures because of multiple recurrences. History of incision and drainage for paraurethral abscess was significantly higher (28.6% vs. 100%, p = 0.002) in patients who had multiple recurrences. CONCLUSIONS: Etiology, fibrosis at local site, and stricture length have significant impact on recurrence of pediatric urethral stricture disease. Associated paraurethral abscess may further compromise the outcome of urethroplasty.

Urethral stricture and stone: their coexistence and management.

PURPOSE: The aim of the study was to determine whether the coexistence of urethral stricture and stone influence the treatment modality of each other and to ascertain the best treatment modality for these group of patients. We also tried to speculate whether the stone is an effect or a cause of the stricture. MATERIALS AND METHODS: Retrospective analysis of prospectively collected data of 35 male patients with coexistent urethral stricture and stone were done between January 1998 and December 2011. Patients were divided in two groups (1 and 2) - limited stone bulk (group 1, n =30) and extensive stone bulk (group 2, n = 5). The former group was treated with endourologic procedures and the latter group managed with open staged procedures. We used ureter scope for endourological management which we think eases the management. RESULTS: Endoscopic management of both stone and stricture were successful in all patients of group 1. Patients of group 2 have been managed by open surgery in two stages. All of them are urologically asymptomatic after a mean of 28 months of follow up. The principle of treatment modality were the bulk of stone, its location and characteristics of stricture. determinants. CONCLUSION: Both stone and stricture can be managed successfully by endoscopic method in most of the patients. Bulk, location of the urethral stone and length of stricture is the main limiting factor for the endoscopic management. A stone can be an "effect" as well as the "cause" of strictured urethra.

Altered immune pathway activity under exercise challenge in Gulf War Illness: an exploratory analysis.

Though potentially linked to the basic physiology of stress response we still have no clear understanding of Gulf War Illness (GWI), a debilitating illness presenting with a complex constellation of immune, endocrine and neurological symptoms. Here we compared male GWI (n=20) with healthy veterans (n=22) and subjects with chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) (n=7). Blood was drawn during a Graded eXercise Test (GXT) prior to exercise, at peak effort (VO2 max) and 4-h post exercise. Affymetrix HG U133 plus 2.0 microarray gene expression profiling in peripheral blood mononuclear cells (PBMCs) was used to estimate activation of over 500 documented pathways. This was cast against ELISA-based measurement of 16 cytokines in plasma and flow cytometric assessment of lymphocyte populations and cytotoxicity. A 2-way ANOVA corrected for multiple comparisons (q statistic <0.05) indicated significant increases in neuroendocrine-immune signaling and inflammatory activity in GWI, with decreased apoptotic signaling. Conversely, cell cycle progression and immune signaling were broadly subdued in CFS. Partial correlation networks linking pathways with symptom severity via changes in immune cell abundance, function and signaling were constructed. Central to these were changes in IL-10 and CD2+ cell abundance and their link to two pathway clusters. The first consisted of pathways supporting neuronal development and migration whereas the second was related to androgen-mediated activation of NF-κB. These exploratory results suggest an over-expression of known exercise response mechanisms as well as illness-specific changes that may involve an overlapping stress-potentiated neuro-inflammatory response.

Preputial/penile skin flap, as a dorsal onlay or tubularized flap: a versatile substitute for complex anterior urethral stricture.

UNLABELLED: Study Type--Therapy (case series) Level of Evidence 4. What's known on the subject? and What does the study add? For long complex anterior urethral stricture augmentation urethroplasty is considered the standard procedure but the best substitute material is still to be ascertained. Preputial/penile skin is a very good substitute especially when used as a dorsal onlay. It demonstrates exceptional functional and cosmetic results even in patients with unsuitable oral mucosa. OBJECTIVE: • To present our experience of single-stage reconstruction of urethral stricture with preputial/penile skin flap, as a dorsal onlay flap (DOF) where there is an adequate urethral plate and as a tubularized flap (TF) where there is a compromised urethral plate, in cases of complex anterior urethral strictures. MATERIALS AND METHODS: • We retrospectively reviewed 144 patients, who underwent single-stage repair of pendular /bulbar urethral strictures with preputial/penile flap as either a DOF or a TF, between January 2001 and December 2008. • Patients were divided into three groups: Group 1 consisted of patients who underwent transverse preputial DOF; Group 2 consisted of those who underwent tube urethroplasty; and Group 3 consisted of those patients who were circumcised and for whom the penile skin was used as a DOF (circumpenile flap). • Patients were followed up by physical examination, retrograde urethrography, uroflowmetry and post-void residual urine measurement. RESULTS: • The mean follow-up was 40.1 months (range 36-84 months). • The primary success rates at 1 year follow-up were 90, 85 and 93.3% for Groups1, 2 and 3, respectively, and at 3-years follow-up they were 85, 75 and 86.7%, respectively. • Half of the recurrences were successfully managed with a single visual internal urethrotomy or dilatation. • The secondary success rate was defined as recurrent stricture managed by a single endoscopic procedure and was 5, 10 and 6.8% in Groups 1, 2 and 3, respectively. The overall success rate was 90.85 and 93.3%, respectively. • A total of 75% of the patients in the study completed 60 months of follow-up with no additional recurrence. CONCLUSIONS: • A preputial/penile flap for complex anterior urethral stricture is a good treatment option, with results similar to other techniques, has acceptable donor site morbidity and is effective even in circumcised patients and for those patients with unsuitable oral mucosa. • A DOF is less likely to lead to diverticula formation and post-void dribbling. TFs have a higher failure rate than DOFs but, when combined judiciously with secondary endoscopic procedures, can provide good results.