Atypical follicular hyperplasia with light chain-restricted germinal centers after COVID-19 booster: a diagnostic pitfall.

There has been a surge in COVID-19 vaccine-associated lymphadenopathy (LAD), including after the booster dose of vaccine. This can create diagnostic dilemmas in oncology patients as the relatively sudden LAD can mimic metastasis or cancer recurrence, at a risk of leading to additional but unnecessary anti-neoplastic therapy. Here we report the histopathologic features in a case of persistent LAD occurring in a patient with history of breast invasive ductal carcinoma which followed a COVID-19 vaccine booster. A needle core and then excisional biopsy showed atypical follicular hyperplasia with features that histologically and phenotypically could mimic follicular lymphoma, but the findings were ultimately interpreted to be reactive in nature and related temporally to COVID-19 vaccine. To our knowledge, this is the first case of an atypical lymphoproliferative lesion with features potentially mimicking lymphoma associated with COVID-19 vaccine.

Development of an innovative intrarenal pressure regulation system for mini-PCNL: A preliminary study.

INTRODUCTION: Miniaturized percutaneous nephrolithotomy (mini-PCNL) requires saline irrigation at high-pressures to maintain visual clarity. However, this may raise the intrarenal pelvic pressures (IRPs) beyond a safe range and may result in a higher complication rate. The aim of this study was to make and validate an automated pressure saline irrigation system to regulate IRPs during mini-PCNL. MATERIALS AND METHODS: A ureteric catheter was connected to an urodynamic machine and the minimum, maximum, and average IRPs reached during a standard 15 Fr mini-PCNL were measured in ten cases. Next, an intrarenal pressure regulation system (IPRS) was conceptualized, designed, patented, and constructed. IPRS was then tested on a mannequin model using the routine instruments. Lastly, the IPRS was evaluated on - five cases of 15 Fr mini-PCNL. The mean maximum IRP as recorded in the baseline data was set as the maximum permissible pressure on IPRS. The efficacy of IPRS was assessed by measuring the IRP, recorded in parallel, on both the IPRS and the urodynamic machine at various stages of the procedure. RESULTS: The mean maximum IRP reached during baseline evaluation was 25 cm of water which was set as the maximum permissible limit of the IPRS. Evaluation of the IRPS on mannequin models and validation clinical cases showed that IPRS measured the IRP accurately and prevented the pressure surge above the set limits Overall, higher IRPs were recorded during stone pulverization as compared to the other surgical steps. CONCLUSIONS: The current IPRS is the first of its kind open platform, portable, automated pressure saline irrigation system. It precisely monitors and controls the IRP and has the potential to reduce the irrigation pressure-related complications.

Clinicopathological Overview of Granulomatous Prostatitis: An Appraisal.

INTRODUCTION: Granulomatous prostatitis is a rare inflammatory condition of the prostate. Granulomatous prostatitis is important because, it mimics prostatic carcinoma clinically and hence the diagnosis can be made only by histopathological examination. AIM: To study the histomorphological features and to know the prevalence of granulomatous prostatitis. MATERIALS AND METHODS: Histopathological records of 1,203 prostatic specimens received in the Department of the Pathology over a period of five years (June 2009 - June 2014). Seventeen cases of histopathologically, diagnosed granulomatous prostatitis were retrieved and reterospective data was collected from the patient's records. RESULTS: Out of 17 cases of granulomatous prostatitis, we encountered 9 cases of non-specific granulomatous prostatitis, 5 cases of xanthogranulomatous prostatitis and 3 cases of specific tubercular prostatitis. The common age ranged from 51-75 years (mean 63 years) with mean PSA level of 15.8ng/ml. Six patients showed focal hypoechoic areas on TRUS and 11 cases revealed hard and fixed nodule on DRE. CONCLUSION: Non-specific granulomatous prostatitis is the most common type of granulomatous prostatitis. There is no specific pattern of clinical, biochemical and ultrasound findings that allows the diagnosis of granulomatous prostatitis or differentiates it from prostatic carcinoma. Hence, histomorphological diagnosis is the gold standard in differentiating various prostatic lesions.

Impact of case volume on outcomes of ureteroscopy for ureteral stones: the clinical research office of the endourological society ureteroscopy global study.

BACKGROUND: The Clinical Research Office of the Endourological Society (CROES) undertook the Ureteroscopy Global Study to establish a prospective global database to examine the worldwide use of ureteroscopy (URS) and to determine factors affecting outcome. OBJECTIVE: To investigate the influence of case volume on the outcomes of URS for ureteral stones. DESIGN, SETTING, AND PARTICIPANTS: The URS Global Study collected prospective data on consecutive patients with urinary stones treated with URS at 114 centres worldwide for 1 yr. Centres were identified as low or high volume based on the median overall annual case volume. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Pre- and intraoperative characteristics, and postoperative outcomes in patients at low- and high-volume centres were compared. The relationships between case volume and stone-free rate (SFR), stone burden, complications, and hospital stay were explored using multivariate regression analysis. RESULTS AND LIMITATIONS: Across all centres, the median case volume was 67; 58 and 56 centres were designated as low volume and high volume, respectively. URS procedures at high-volume centres took significantly less time to conduct. Mean SFR was 91.9% and 86.3% at high- and low-volume centres, respectively (p<0.001); the adjusted probability of a stone-free outcome increased with increasing case volume (p<0.001). Patients treated at a high-volume centre were less likely to need retreatment, had shorter postoperative hospital stay, were less likely to be readmitted within 3 mo, and had fewer and less severe complications. At case volumes approximately >200, the probability of complications decreased with increasing case volume (p=0.02). The study is limited by the heterogeneity of participating centres and surgeons and the inclusion of patients treated by more than one approach. CONCLUSIONS: In the treatment of ureteral stones with URS, high-volume centres achieve better outcomes than low-volume centres. Several outcome measures for URS improve with an increase in case volume. PATIENT SUMMARY: Outcomes following treatment of ureteral stones by ureteroscopy (URS) were studied in a large group of patients at centres worldwide. The proportion of successful procedures (ie, those in which patients became stone free) increased as the annual volume of URS at a hospital increased. Hospital stays were shorter and postoperative complications were less likely at high-volume hospitals. We conclude that for URS, the best outcomes are seen in patients treated at high-volume hospitals.

Stability-indicating LC-UV method for the determination of eszopiclone and degradation impurities in tablet dosage form.

A sensitive, stability-indicating reversed-phase high-performance liquid chromatographic method was developed for the determination of eszopiclone and related impurities in tablet dosage form. The chromatographic separation was achieved on an Inertsil C18 column (250 × 4.6 mm, 5 µm), using a mobile phase consisting of 0.05M monobasic sodium phosphate buffer containing 0.8% sodium lauryl sulfate (pH 3.5) and acetonitrile in the ratio of 60:40 (v/v), at a flow rate of 1.5 mL/min and temperature of 40°C. Quantification was achieved with photodiode array detection at 303 nm. The described method showed excellent linearity over a range of limits of quantification to 4.8 µg/mL (150% of specification limit; i.e., 3.2 µg/mL). The drug product was subjected to the stress conditions of oxidative, acid, base, thermal and photolytic degradation. Eszopiclone degradation was observed in acid hydrolysis, base hydrolysis and peroxide stress conditions. Eszopiclone was stable in thermal and photolytic degradation conditions. The developed method is simple, selective and accurate for the quantification of impurities and degradation products of eszopiclone in tablet dosage form.

A novel paraboloid intracorporeal lithotripter: computer aided design analysis and in vitro comparison with holmium laser for large renal calculi.

PURPOSE: An intracorporeal lithotripsy probe tip was designed with a paraboloid shaped tip and compared with holmium laser for stone pulverization. MATERIALS AND METHODS: The paraboloid tip concept was developed and designed using computer aided design (CAD), fabricated, and patented. CAD analysis and in vitro comparison (with laser) of pulverization and propulsion dynamics were performed in an underwater hands-free bench arrangement using phantom stones. SPSS analysis for different energy cohorts was performed. RESULTS: CAD analysis: At "point contact" with the tip, the paraboloid lithotripter generated 3590 bars at generator settings of 4 bars. During "follow-up impacts," the tip pressure exponentially decreased (graduated tip pressure) and the lateral/centrifugal forces increased, converting the probe into a side-firing energy source. Bench analysis: At point contact, the paraboloid lithotripter at 2, 3, and 4 bars was comparable to that of a 6, 10, and 15 W laser, respectively (P<0.005). The paraboloid lithotripter showed a statistically significant advantage in breaking the phantoms, as against a laser that always bored through the phantom. Stone propulsion was comparable within all energy cohorts (P>0.05). CONCLUSION: The paraboloid lithotripter generates highly focused impact force with low propulsion, at point contact. As stone pulverization progresses, the tip forces exponentially decrease and the probe converts into a lateral firing energy source resulting in pulverization into larger fragments. Thus, the paraboloid lithotripter has all the advantages of laser at point contact and advantages of pneumatic lithotripter at follow-up hits, akin to being a bimodal energy source.

A human tRNA methyltransferase 9-like protein prevents tumour growth by regulating LIN9 and HIF1-α.

Emerging evidence points to aberrant regulation of translation as a driver of cell transformation in cancer. Given the direct control of translation by tRNA modifications, tRNA modifying enzymes may function as regulators of cancer progression. Here, we show that a tRNA methyltransferase 9-like (hTRM9L/KIAA1456) mRNA is down-regulated in breast, bladder, colorectal, cervix and testicular carcinomas. In the aggressive SW620 and HCT116 colon carcinoma cell lines, hTRM9L is silenced and its re-expression and methyltransferase activity dramatically suppressed tumour growth in vivo. This growth inhibition was linked to decreased proliferation, senescence-like G0/G1-arrest and up-regulation of the RB interacting protein LIN9. Additionally, SW620 cells re-expressing hTRM9L did not respond to hypoxia via HIF1-α-dependent induction of GLUT1. Importantly, hTRM9L-negative tumours were highly sensitive to aminoglycoside antibiotics and this was associated with altered tRNA modification levels compared to antibiotic resistant hTRM9L-expressing SW620 cells. Our study links hTRM9L and tRNA modifications to inhibition of tumour growth via LIN9 and HIF1-α-dependent mechanisms. It also suggests that aminoglycoside antibiotics may be useful to treat hTRM9L-deficient tumours.

A validated stability-indicating liquid chromatographic method for determination of degradation impurities and diastereomers in voriconazole tablets.

A reversed-phase gradient liquid chromatographic method has been developed for the quantitative determination of Voriconazole, along with its degradation and diastereomeric impurities in tablet dosage form. Chromatographic separation has been achieved on an Inertsil ODS 3V, 150 × 4.6 mm, 5 µm column. The mobile phase consisting of solvent A 0.05 molar (M) potassium dihydrogen phosphate (pH 2.5 buffer) and solvent B (mixture of acetonitrile and methanol in the ratio 90:10 (v/v)), was delivered at a flow rate of 1.2 mL min(-1) with the detection wavelength at 256 nm. Resolution of Voriconazole and all five potential impurities was achieved at greater than 2.0 for all pairs of compounds. The drug was subjected to stress conditions such as oxidative, acid and base hydrolysis, and thermal and photolytic degradation. Voriconazole was found to degrade significantly under base hydrolysis stress conditions compared to acid hydrolysis stress conditions. The degradation products were well-resolved from the main peak and its impurities, thus proving the stability-indicating power of the method. The stressed samples were assayed against a reference standard and the mass balance was found to be close to 99.0%. The developed method was validated as per ICH guidelines with respect to specificity, linearity, limit of detection, limit of quantification, accuracy, precision, and robustness.

Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response.

S-phase and DNA damage promote increased ribonucleotide reductase (RNR) activity. Translation of RNR1 has been linked to the wobble uridine modifying enzyme tRNA methyltransferase 9 (Trm9). We predicted that changes in tRNA modification would translationally regulate RNR1 after DNA damage to promote cell cycle progression. In support, we demonstrate that the Trm9-dependent tRNA modification 5-methoxycarbonylmethyluridine (mcm(5)U) is increased in hydroxyurea (HU)-induced S-phase cells, relative to G(1) and G(2), and that mcm(5)U is one of 16 tRNA modifications whose levels oscillate during the cell cycle. Codon-reporter data matches the mcm(5)U increase to Trm9 and the efficient translation of AGA codons and RNR1. Further, we show that in trm9Δ cells reduced Rnr1 protein levels cause delayed transition into S-phase after damage. Codon re-engineering of RNR1 increased the number of trm9Δ cells that have transitioned into S-phase 1 h after DNA damage and that have increased Rnr1 protein levels, similar to that of wild-type cells expressing native RNR1. Our data supports a model in which codon usage and tRNA modification are regulatory components of the DNA damage response, with both playing vital roles in cell cycle progression.

Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications.

Correct codon-anticodon pairing promotes translational fidelity, with these interactions greatly facilitated by modified nucleosides found in tRNA. We hypothesized that wobble uridine modifications catalyzed by tRNA methyltransferase 9 (Trm9) are essential for translational fidelity. In support, we have used phenotypic, reporter and protein-based assays to demonstrate increased translational infidelity in trm9Δ Saccharomyces cerevisiae cells. Codon reengineering studies suggest that Trm9-catalyzed tRNA modifications promote fidelity during the translation of specific genes, those rich in arginine and glutamic acid codons from mixed boxes. Using quantitative tRNA modification analysis, we determined that trm9Δ cells are only deficient in 2 of 23 tRNA modifications, with those 2, 5-methoxycarbonylmethyluridine (mcm ( 5) U) and 5-methoxycarbonylmethyl-2-thiouridine (mcm ( 5) s ( 2) U), classified as key determinants of translational fidelity. We also show that in the absence of mcm ( 5) U and mcm ( 5) s ( 2) U, the resulting translational infidelity promotes protein errors and activation of unfolded protein and heat shock responses. These data support a model in which Trm9-catalyzed tRNA modifications promote fidelity during the translation of specific transcripts, with decreased wobble base modification leading to translational infidelity, protein errors and activation of protein stress response pathways.

The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes.

A codon consists of three nucleotides and functions during translation to dictate the insertion of a specific amino acid in a growing peptide or, in the case of stop codons, to specify the completion of protein synthesis. There are 64 possible single codons and there are 4096 double, 262 144 triple, 16 777 216 quadruple and 1 073 741 824 quintuple codon combinations available for use by specific genes and genomes. In order to evaluate the use of specific single, double, triple, quadruple and quintuple codon combinations in genes and gene networks, we have developed a codon counting tool and employed it to analyze 5780 Saccharomyces cerevisiae genes. We have also developed visualization approaches, including codon painting, combination and bar graphs, and have used them to identify distinct codon usage patterns in specific genes and groups of genes. Using our developed Gene-Specific Codon Counting Database, we have identified extreme codon runs in specific genes. We have also demonstrated that specific codon combinations or usage patterns are over-represented in genes whose corresponding proteins belong to ribosome or translation-associated biological processes. Our resulting database provides a mineable list of multi-codon data and can be used to identify unique sequence runs and codon usage patterns in individual and functionally linked groups of genes.

In vitro assessment of a novel spearheaded pneumatic intracorporeal lithotriptor.

BACKGROUND AND PURPOSE: Intracorporeal lithotripsy is an important modality used for stone pulverization. To improve the pulverization properties of intracorporeal lithotriptors, a novel intracorporeal "spearheaded lithotriptor" was designed by our institute. It was compared in vitro with the conventional lithotriptor. MATERIALS AND METHODS: The pulverization and propulsion dynamics were evaluated at various pressure settings on an in vitro bench arrangement with phantom stones. Lateral displacement during pulverization was also compared. RESULTS: The spearheaded lithotriptor had a better first hit (P<0.001) and follow-up hit dynamics (P<0.01). Stone propulsion and lateral displacement were low for the spearheaded lithotriptor at all pressure settings (P<0.05). CONCLUSION: The spearheaded lithotriptor improved stone pulverization without increasing the risk of stone migration. Further clinical evaluation of this novel probe is necessary.

Cross-species Functionome analysis identifies proteins associated with DNA repair, translation and aerobic respiration as conserved modulators of UV-toxicity.

Cellular responses to DNA damage can prevent mutations and death. In this study, we have used high throughput screens and developed a comparative genomic approach, termed Functionome mapping, to discover conserved responses to UVC-damage. Functionome mapping uses gene ontology (GO) information to link proteins with similar biological functions from different organisms, and we have used it to compare 303, 311 and 288 UVC-toxicity modulating proteins from Escherichia coli, Schizosaccharomyces pombe and Saccharomyces cerevisiae, respectively. We have demonstrated that all three organisms use DNA repair, translation and aerobic respiration associated processes to modulate the toxicity of UVC, with these last two categories highlighting the importance of ribosomal proteins and electron transport machinery. Our study has demonstrated that comparative genomic approaches can be used to identify conserved responses to damage, and suggest roles for translational machinery and components of energy metabolism in optimizing the DNA damage response.

A novel 5-part Percutaneous Access Needle with Glidewire technique (5-PANG) for percutaneous nephrolithotomy: our initial experience.

OBJECTIVES: To describe the use of an innovative 5-part Percutaneous Access Needle with Glidewire (5-PANG), a novel technique in an attempt to make percutaneous nephrolithotomy (PCNL-a routinely performed procedure) tract establishment a fast, safe, and less cumbersome procedure. METHODS: An access needle (5-PANG needle) was designed and fabricated at the Institute of Urology, Dhule, and used for percutaneous renal access during PCNL. RESULTS: The 5-PANG technique was used in 55 cases (57 renal units). It was used for all calyceal punctures, all types of stones, renal anatomies, and for second-time surgeries (8 cases). The mean time required (from the stage of the successful puncture using the first 3 parts of the needle till the placement of Alken's rod) was 44.54 seconds. The radiation time was a mean of 3.34 seconds. Punctured calyx and tract size did not affect the results. Visual clarity was good in 85.9% cases. No case had to be converted to conventional method or abandoned. There were no intra- or postoperative complications related to the 5-PANG. CONCLUSIONS: We find the 5-PANG technique safe, fast, effective, and inexpensive. It is easy to learn and master. We recommend this technique over the standard initial tract dilatation techniques.

Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks.

The identification of cellular responses to damage can promote mechanistic insight into stress signalling. We have screened a library of 3968 Escherichia coli gene-deletion mutants to identify 99 gene products that modulate the toxicity of the alkylating agent methyl methanesulfonate (MMS). We have developed an ontology mapping approach to identify functional categories over-represented with MMS-toxicity modulating proteins and demonstrate that, in addition to DNA re-synthesis (replication, recombination, and repair), proteins involved in mRNA processing and translation influence viability after MMS damage. We have also mapped our MMS-toxicity modulating proteins onto an E. coli protein interactome and identified a sub-network consisting of 32 proteins functioning in DNA repair, mRNA processing, and translation. Clustering coefficient analysis identified seven highly connected MMS-toxicity modulating proteins associated with translation and mRNA processing, with the high connectivity suggestive of a coordinated response. Corresponding results from reporter assays support the idea that the SOS response is influenced by activities associated with the mRNA-translation interface.

A molecular bar-coded DNA repair resource for pooled toxicogenomic screens.

DNA damage from exogenous and endogenous sources can promote mutations and cell death. Fortunately, cells contain DNA repair and damage signaling pathways to reduce the mutagenic and cytotoxic effects of DNA damage. The identification of specific DNA repair proteins and the coordination of DNA repair pathways after damage has been a central theme to the field of genetic toxicology and we have developed a tool for use in this area. We have produced 99 molecular bar-coded Escherichia coli gene-deletion mutants specific to DNA repair and damage signaling pathways, and each bar-coded mutant can be tracked in pooled format using bar-code specific microarrays. Our design adapted bar-codes developed for the Saccharomyces cerevisiae gene-deletion project, which allowed us to utilize an available microarray product for pooled gene-exposure studies. Microarray-based screens were used for en masse identification of individual mutants sensitive to methyl methanesulfonate (MMS). As expected, gene-deletion mutants specific to direct, base excision, and recombinational DNA repair pathways were identified as MMS-sensitive in our pooled assay, thus validating our resource. We have demonstrated that molecular bar-codes designed for S. cerevisiae are transferable to E. coli, and that they can be used with pre-existing microarrays to perform competitive growth experiments. Further, when comparing microarray to traditional plate-based screens both overlapping and distinct results were obtained, which is a novel technical finding, with discrepancies between the two approaches explained by differences in output measurements (DNA content versus cell mass). The microarray-based classification of Deltatag and DeltadinG cells as depleted after MMS exposure, contrary to plate-based methods, led to the discovery that Deltatag and DeltadinG cells show a filamentation phenotype after MMS exposure, thus accounting for the discrepancy. A novel biological finding is the observation that while DeltadinG cells filament in response to MMS they exhibit wild-type sulA expression after exposure. This decoupling of filamentation from SulA levels suggests that DinG is associated with the SulA-independent filamentation pathway.

Trm9-catalyzed tRNA modifications link translation to the DNA damage response.

Transcriptional and posttranslational signals are known mechanisms that promote efficient responses to DNA damage. We have identified Saccharomyces cerevisiae tRNA methyltransferase 9 (Trm9) as an enzyme that prevents cell death via translational enhancement of DNA damage response proteins. Trm9 methylates the uridine wobble base of tRNAARG(UCU) and tRNAGLU(UUC). We used computational and molecular approaches to predict that Trm9 enhances the translation of some transcripts overrepresented with specific arginine and glutamic acid codons. We found that translation elongation factor 3 (YEF3) and the ribonucleotide reductase (RNR1 and RNR3) large subunits are overrepresented with specific arginine and glutamic acid codons, and we demonstrated that Trm9 significantly enhances Yef3, Rnr1, and Rnr3 protein levels. Additionally, we identified 425 genes, which included YEF3, RNR1, and RNR3, with a unique codon usage pattern linked to Trm9. We propose that Trm9-specific tRNA modifications enhance codon-specific translation elongation and promote increased levels of key damage response proteins.