PanDelos-frags: A methodology for discovering pangenomic content of incomplete microbial assemblies

Pangenomics was originally defined as the problem of comparing the composition of genes into gene families within a set of bacterial isolates belonging to the same species. The problem requires the calculation of sequence homology among such genes. When combined with metagenomics, namely for human microbiome composition analysis, gene-oriented pangenome detection becomes a promising method to decipher ecosystem functions and population-level evolution. Established computational tools are able to investigate the genetic content of isolates for which a complete genomic sequence is available. However, there is a plethora of incomplete genomes that are available on public resources, which only a few tools may analyze. Incomplete means that the process for reconstructing their genomic sequence is not complete, and only fragments of their sequence are currently available. However, the information contained in these fragments may play an essential role in the analyses. Here, we present PanDelos-frags, a computational tool which exploits and extends previous results in analyzing complete genomes. It provides a new methodology for inferring missing genetic information and thus for managing incomplete genomes. PanDelos-frags outperforms state-of-the-art approaches in reconstructing gene families in synthetic benchmarks and in a real use case of metagenomics. PanDelos-frags is publicly available at https://github.com/InfOmics/PanDelos-frags.

Connectivity changes in major depressive disorder after rTMS: a review of functional and structural connectivity data

Aims

In the search for effective therapeutic strategies for depression, repetitive transcranial magnetic stimulation (rTMS) emerged as a non-invasive, promising treatment. This is because the antidepressant effect of rTMS might be related to neuronal plasticity mechanisms possibly reverting connectivity alterations often observed in depression. Therefore, in this review, we aimed at providing an overview of the findings reported by studies investigating functional and structural connectivity changes after rTMS in depression.

Methods

A bibliographic search was conducted on PubMed, including studies that used unilateral, excitatory (⩾10 Hz) rTMS treatment targeted on the left dorsolateral prefrontal cortex (DLPFC) in unipolar depressed patients.

Results

The majority of the results showed significant TMS-induced changes in functional connectivity (FC) between areas important for emotion regulation, including the DLPFC and the subgenual anterior cingulate cortex, and among regions that are part of the major resting-state networks, such as the Default Mode Network, the Salience Networks and the Central Executive Network. Finally, in diffusion tensor imaging studies, it has been reported that rTMS appeared to increase fractional anisotropy in the frontal lobe.

Limitations

The small sample size, the heterogeneity of the rTMS stimulation parameters, the concomitant use of psychotropic drugs might have limited the generalisability of the results.

Conclusions

Overall, rTMS treatment induces structural and FC changes in brain regions and networks implicated in the pathogenesis of unipolar depression. However, whether these changes underlie the antidepressant effect of rTMS still needs to be clarified.

P–095 Outcomes and predictive factors of successful salvage microdissection testicular sperm extraction (mTESE) after failed TESE in men with non-obstructive azoospermia: results from a multicenter study

Study question

We assessed the outcome and predictors of successful salvage microdissection testicular sperm extraction (mTESE) in non-obstructive azoospermia (NOA) men previously submitted to unfruitful classic (cTESE).

Summary answer

The sperm retrieval rate at salvage mTESE was almost 50%. Hypospermatogenesis and low FSH values were associated with positive outcomes at salvage mTESE

What is known already

In men with NOA testicular sperm can be retrieved using cTESE in approximately 50% of cases. mTESE has been proposed as a salvage treatment option for men with a previously failed TESE, but data are scarce.

Study design, size, duration

Multicenter, cross-sectional study. Complete data from 61 NOA men who underwent mTESE after a failed cTESE between 01/2014 and 10/2020, at 6 tertiary referral centers in Italy were analysed.

Participants/materials, setting, methods

All men underwent testicular ultrasound, hormonal and genetic blood testing. Histopathological diagnosis from TESE was collected in every man. Semen analyses were based on the 2010 WHO reference criteria. mTESE was performed according to the technique of Schlegel et al. (1999). Descriptive statistics and logistic regression models were used to investigate potential predictors of positive sperm retrieval (SR+) after salvage mTESE.

Main results and the role of chance

Overall, median (IQR) age and testicular volume were 35 (31–38) years and 10 (6–15) ml, respectively. Baseline serum FSH and total testosterone levels were 17.1 (8.6–30.4) mUI/mL and 4.7 (3.5–6.4) ng/mL, respectively. Sertoli-cell-only (SCO) syndrome, maturation arrest (MA) and hypospermatogenesis were found in 24 (39.3%), 21 (34.4%) and 16 (26.2%) men after cTESE, respectively. Spermatozoa were retrieved in 30 (49.2%) men at salvage mTESE. Patients with a diagnosis of hypospermatogenesis had a higher rate of SR + [12/16 (75%)] than those with MA [12/21 (57.1%)] and SCOS [6/24 (25%)] after salvage mTESE (p < 0.01), which was bilateral in 36 (59%) cases. FSH was higher [16.5 (8–22) vs. 8.9 (5–13) mUI/mL, p < 0.01] in SR- patients compared to SR+. No difference in clinical characteristics was found between patients with SR+ and SR- at salvage mTESE. There were no significant complications after mTESE. Multivariable logistic regression analysis showed that hypospermatogenesis (OR 9.7; p < 0.01) and low FSH levels (OR 0.9, p < 0.001) were independent predictors of SR+ after salvage mTESE, after accounting for age.

Limitations, reasons for caution

Despite we analysed one of the largest series of salvage mTESE, the samples size is too small to draw general conclusions. Because of the multicenter nature of the study we cannot rely on standardization of surgical techniques for TESE.

Wider implications of the findings: This is one of the larger studies on salvage mTESE. The selection of patients for salvage mTESE is of critical importance.

Trial registration number

na

Use of the BioFire Film Array Blood Culture Identification(BCID) Panel(BioFire Diagnostics, Salt Lake City, Utah) on Pleural Fluid Samples in Pediatric Patients Hospitalized for Community Acquired Pneumonia(CAP)

Introduction/Objective

CAP accounts for approximately 124,000 pediatric hospitalizations annually. Those patients often have received antibiotics prior to admission. Many have concurrent viral infections. Bacterial infections accompanying viral respiratory infections are known to increase morbidity and mortality. Traditional bacterial culture methods are often negative because of previous antibiotic therapy. The BCID, a multiplex polymerase chain reaction(PCR) assay, can identify 19 bacterial pathogens in approximately 90 minutes. It is FDA approved for blood culture isolates. We hypothesized it would detect bacterial pathogens in pleural effusions.

Methods

BCID panels were done on residual pleural fluid samples from 10 patients with severe community acquired pneumonia during the period 5/2018 – 12/2019. The patients had positive radiographic findings of pneumonia, were inpatients, had intact immune systems by clinical history and had received antibiotic therapy for more than 8 hours before specimen collection. Treatment required 133 inpatient days. 6 of 10 were diagnosed with viral respiratory pathogens. 1 of 9 had a positive blood culture. 1 of 10 had a positive pleural fluid culture.

Results

10 of 10 pleural fluid specimens were positive for a pathogen on the BCID panel – 8, Streptococcus pneumoniae, 1, Staphylococcus aureus and I, Streptococcus pyogens. Two of ten had confirmatory positive cultures. Also, one pleural fluid gram stain showed gram positive cocci in chains and clusters. The BCID detected Streptococcus pyogens. Anti Streptolysin O was strongly positive, 964(0 – 70) IU/mL.

Conclusion

The yield of bacterial culture plummets with previous antibiotic treatment. FDA approved multiplex PCR panels have narrowly defined specimen requirements. That increases the cost and decreases test applicability.

Despite a history of appropriate immunizations in the sample population Streptococcus pneumoniae may be prevalent in the complex pediatric pneumonia population. The BCID may be effective at pathogen detection in cases of complex pneumonia where patients have received prior antibiotic treatment.

Molecular docking, design, synthesis and biological evaluation of novel 2,3-aryl-thiazolidin-4-ones as potent NNRTIs

Nonnucleoside reverse transcriptase inhibitors (NNRTIs) remain the most promising anti-AIDS agents that target the HIV-1 reverse transcriptase enzyme (RT). However, the efficiency of approved NNRTI drugs has decreased by the appearance of drug-resistant viruses and side effects upon long-term usage. Thus, there is an urgent need for developing new, potent NNRTIs with broad spectrum against HIV-1 virus and with improved properties. In this study, a series of thiazolidinone derivatives was designed based on a butterfly mimicking scaffold consisting of a substituted benzothiazolyl moiety connected with a substituted phenyl ring via a thiazolidinone moiety. The most promising derivatives were selected using molecular docking analysis and PASS prediction program, synthesized and evaluated for HIV-1 RT inhibition. Five out of fifteen tested compounds exhibited good inhibitory action. It was observed that the presence of Cl or CN substituents at the position 6 of the benzothiazole ring in combination with two fluoro atoms at the ortho-positions or a hydrogen acceptor substituent at the 4-position of the phenyl ring are favourable for the HIV RT inhibitory activity.

Statistical mechanical properties of sequence space determine the efficiency of the various algorithms to predict interaction energies and native contacts from protein coevolution

Studying evolutionary correlations in alignments of homologous sequences by means of an inverse Potts model has proven useful to obtain residue-residue contact energies and to predict contacts in proteins. The quality of the results depend much on several choices of the detailed model and on the algorithms used. We built, in a very controlled way, synthetic alignments with statistical properties similar to those of real proteins, and used them to assess the performance of different inversion algorithms and of their variants. Realistic synthetic alignments display typical features of low-temperature phases of disordered systems, a feature that affects the inversion algorithms. We showed that a Boltzmann-learning algorithm is computationally feasible and performs well in predicting the energy of native contacts. However, all algorithms, when applied to alignments of realistic size, suffer of false positives quite equally, making the quality of the prediction of native contacts with the different algorithm much system-dependent.

Repair of transperineal recto-urethral fistula using a fibrin sealant haemostatic patch

AIM

Recto-urethral fistula (RUF) is a rare complication of radical prostatectomy. We report a transperineal approach using a fibrin sealant haemostatic patch.

METHOD

Five consecutive patients who developed RUF following radical prostatectomy had a direct transperineal repair with a haemostatic patch (TachoSil®) and were assessed at a median follow-up of 35.5 (21-45) months.

RESULTS

There were no early postoperative complications. The average length of hospital stay was 5 (4-7) days. One patient developed recurrence 4 weeks after removal of the urethral catheter. Following healing in four patients the stoma was reversed at a median interval of 3 months, and 9.5 (7-10) months following the prostatic surgery. In the four patients with successful closure there was no case of recurrence or anorectal or urinary dysfunction at a median follow-up of 35.5 (21-45) months.

CONCLUSION

Direct transperineal repair of RUF reinforced with a fibrin haemostatic patch of TachoSil is safe and effective.

Diagnostic value of qualitative and strain ratio elastography in the differential diagnosis of non-palpable testicular lesions

The purpose of this study was to evaluate prospectively the accuracy of qualitative and strain ratio elastography (SE) in the differential diagnosis of non‐palpable testicular lesions. The local review board approved the protocol and all patients gave their consent. One hundred and six patients with non‐palpable testicular lesions were consecutively enrolled. Baseline ultrasonography (US) and SE were correlated with clinical and histological features and ROC curves developed for diagnostic accuracy. The non‐palpable lesions were all ≤1.5 cm; 37/106 (34.9%) were malignant, 38 (35.9%) were benign, and 31 (29.2%) were non‐neoplastic. Independent risk factors for malignancy were as follows: size (OR 17.788; p = 0.002), microlithiasis (OR 17.673, p < 0.001), intralesional vascularization (OR 9.207, p = 0.006), and hypoechogenicity (OR, 11.509, p = 0.036). Baseline US had 89.2% sensitivity (95% CI 74.6–97.0) and 85.5% specificity (95% CI 75.0–92.8) in identifying malignancies, and 94.6% sensitivity (95% CI 86.9–98.5) and 87.1% specificity (95% CI 70.2–96.4) in discriminating neoplasms from non‐neoplastic lesions. An elasticity score (ES) of 3 out of 3 (ES3, maximum hardness) was recorded in 30/37 (81.1%) malignant lesions (p < 0.001). An intermediate score of 2 (ES2) was recorded in 19/38 (36.8%) benign neoplastic lesions and in 22/31 (71%) non‐neoplastic lesions (p = 0.005 and p = 0.001 vs. malignancies). None of the non‐neoplastic lesions scored ES3. Logistic regression analysis revealed a significant association between ES3 and malignancy (χ² = 42.212, p < 0.001). ES1 and ES2 were predictors of benignity (p < 0.01). Overall, SE was 81.8% sensitive (95% CI 64.8–92.0) and 79.1% specific (95% CI 68.3–88.4) in identifying malignancies, and 58.6% sensitive (95% CI 46.7–69.9) and 100% specific (95% CI 88.8–100) in discriminating non‐neoplastic lesions. Strain ratio measurement did not improve the accuracy of qualitative elastography. Strain ratio measurement offers no improvement over elastographic qualitative assessment of testicular lesions; testicular SE may support conventional US in identifying non‐neoplastic lesions when findings are controversial, but its added value in clinical practice remains to be proven.

Registered Replication Report: Schooler and Engstler-Schooler (1990)

Trying to remember something now typically improves your ability to remember it later. However, after watching a video of a simulated bank robbery, participants who verbally described the robber were 25% worse at identifying the robber in a lineup than were participants who instead listed U.S. states and capitals-this has been termed the "verbal overshadowing" effect (Schooler & Engstler-Schooler, 1990). More recent studies suggested that this effect might be substantially smaller than first reported. Given uncertainty about the effect size, the influence of this finding in the memory literature, and its practical importance for police procedures, we conducted two collections of preregistered direct replications (RRR1 and RRR2) that differed only in the order of the description task and a filler task. In RRR1, when the description task immediately followed the robbery, participants who provided a description were 4% less likely to select the robber than were those in the control condition. In RRR2, when the description was delayed by 20 min, they were 16% less likely to select the robber. These findings reveal a robust verbal overshadowing effect that is strongly influenced by the relative timing of the tasks. The discussion considers further implications of these replications for our understanding of verbal overshadowing.

Allium stent for treatment of ureteral stenosis

AIM

The aim of our study is to value the efficacy of self-expanding Allium ureteral stent in the treatment of ureteral stenosis.

METHODS

From 2010 to 2013, we treated 12 patients, aged from 23 to 64 years. Six patients were affected by congenital UPJ obstruction, four patients by iatrogenic unilateral ureteral stenosis and two patients by bilateral ureteral stenosis. All the patients showed hydronephrosis before the stenotic lesion and pain. In all the patients, we use a 30 Fr, 10 cm length self-expanding Allium ureteral stent. The medium follow-up is 10 months after Allium stent removal.

RESULTS

All the patients were immediately free of pain after the procedure. We didn't experience intra, peri and postoperative complications. In all the patients, a complete correction of the stenotic lesion was obtained. No recurrence of stenosis occurred during follow-up.

CONCLUSION

Self-expanding allium ureteral stent represents an effective treatment of ureteral stenosis in patients not suitable for surgery.

[Duane vertical surgical treatment]

CASE REPORT

We report 3 cases with a vertical incomitance in upgaze, narrowing of palpebral fissure, and pseudo-overaction of both inferior oblique muscles. Surgery consisted of an elevation of both lateral rectus muscles with an asymmetrical weakening. A satisfactory result was achieved in 2 cases, whereas a Lambda syndrome appeared in the other case.

DISCUSSION

The surgical technique of upper-insertion with a recession of both lateral rectus muscles improved vertical incomitance in 2 of the 3 patients; however, a residual deviation remains in the majority of cases.

A pioneer of public health, Bernardino Ramazzini

2014 marks the tercentenary of the death of Bernardino Ramazzini, an academic who lived in the Duchy of Modena in the second half of the seventeenth century. This event represents an occasion to remember his thinking, which is remarkably anticipatory of some concepts and trends of modern public health. Although the main merit of Bernardino Ramazzini lies in his contribution to the knowledge of occupational diseases, which granted him the title of father of Occupational Medicine, his work deserves a more detailed and complete consideration. In fact, the systematic approach to the clinical presentation of diseases and their relationship to work, gathered in the famed treatise De Morbis Artificum Diatriba, resulted in little attention being paid to the preventive aspects of his thinking. The free spirit, the tension for searching, the love for the discussion characterize his scientific attitude, which spans from the anticipation of an epidemiologic approach to studies on the impact of air and climate, from workplace surveillance to suggestions for the protection of health, from proposals of primary prevention tools to recommendations of lifestyle behaviour, from educational issues to health promotion. His scientific, cultural and humanitarian stature is evidenced by his overall scientific works revealing the modernity of his thinking in the light of the present trend of public health focusing on the needs of people and promoting occupational health as an integral component of the health concept.

[The cultural, economic and social context of Ramazzini's Diatriba in the second half of the 17th century--in memory of Pericle Di Pietro on occasion of the third centenary of the publication of the final edition of the Diatriba (Padua, 1713)]

The paper aims at analyzing the development of Ramazzini's train of thought in Diatriba within the cultural, economic and social context of the Duchy of Modena in the second half of the seventeenth century. The period was characterized by a deep recession affecting every aspect of life in the territory: culture was mostly at the service of the court's image, the economy, mainly based on agriculture, was in crisis and many crafts depended on the demands of the nobility. The culture of the Este court had, however, little influence on Ramazzini's ideas, whereas social and economic aspects were the stimulus to his experimentalism via observation. In this context, Ramazzini was an illuminated nonconformist, who analysed the vulnerability of the population with an anthropological approach that embraced individuals, environment, social and economic status.

Occupation and breast cancer: fitness for work is an aspect that needs to be addressed

Much progress has been made in breast cancer prevention, treatment and rehabilitation and there is evidence that the majority of breast cancer survivors are able to continue working. Although several studies suggest that environmental and occupational factors (certain chemicals and circadian rhythm changes) contribute to the onset of breast cancer, current management of individuals susceptible to breast cancer and breast cancer survivors does not focus on either occupational exposure or working conditions. A more active role of physicians in informing patients about occupational hazards and of occupational health physicians in making appropriate fitness for work judgments would lead to a more complete assessment ofthe health risk of susceptible workers and workers resuming their activity after sick leave for breast cancer treatment.

Genetics of cerebral hemorrhage and microbleeds

Intracerebral haemorrhage (ICH) is the least treatable and often fatal form of stroke. Literature data suggest a strong familial contribution to ICH. The identification of genetic factors with a role in ICH could enhance the understanding of the pathogenesis of hemorrhagic brain injury leading to new treatment and prevention approaches with the final goal of identifying high risk individuals in which genetic pattern may influence clinical and therapeutical decisions. Herein, we provide an updated review on genetic factors associated with occurrence and outcome of ICH. Except for monogenic disease which account for a minor proportion of hemorrhages, most of hemorrhagic stroke heritability is believed to be polygenic. However, the results of candidate gene studies did not show significant results except for the association between apoE genotype and ICH, which has been replicated in large population studies. These data may support the hypothesis that the risk that can be attributed to each of these polymorphisms taken individually is still moderate and some relatively common variants could contribute in determining the disease acting in synergy with other genetic factors.

A dictionary based informational genome analysis

Background

In the post-genomic era several methods of computational genomics are emerging to understand how the whole information is structured within genomes. Literature of last five years accounts for several alignment-free methods, arisen as alternative metrics for dissimilarity of biological sequences. Among the others, recent approaches are based on empirical frequencies of DNA k-mers in whole genomes.

Results

Any set of words (factors) occurring in a genome provides a genomic dictionary. About sixty genomes were analyzed by means of informational indexes based on genomic dictionaries, where a systemic view replaces a local sequence analysis. A software prototype applying a methodology here outlined carried out some computations on genomic data. We computed informational indexes, built the genomic dictionaries with different sizes, along with frequency distributions. The software performed three main tasks: computation of informational indexes, storage of these in a database, index analysis and visualization. The validation was done by investigating genomes of various organisms. A systematic analysis of genomic repeats of several lengths, which is of vivid interest in biology (for example to compute excessively represented functional sequences, such as promoters), was discussed, and suggested a method to define synthetic genetic networks.

Conclusions

We introduced a methodology based on dictionaries, and an efficient motif-finding software application for comparative genomics. This approach could be extended along many investigation lines, namely exported in other contexts of computational genomics, as a basis for discrimination of genomic pathologies.

Isolation and characterization of canine parvovirus type 2C (CPV-2C) from symptomatic puppies

Canine parvovirus type 2 (CPV-2) is a leading cause of diarrhea in puppies in several parts of the world. In this study CPV-2 was detected and recovered from puppies showing clinical disease from Montevideo, Uruguay. Samples were processed and used to infect CRFK and MDCK cells in order to isolate the virus. Out of twelve, two samples were positive for CPV-2. A genomic region of 583 bp was amplified and the molecular characterization was performed by sequencing, phylogenetic analysis and Restriction Fragment Length Polymorphism (RFLP). Two isolated viruses (UY1 and UY2) were CPV-2c-like viruses. The comparison between the cytophatic effect (CPE) of CPV-2 (vaccinal virus) and CPV-2c (isolated virus) on primary canine cells cultures and on CRFK line cells, demonstrated that CPV-2c is less citopathogenic in CRFK than in primary cultures. Our study represents the first report on isolation and characterization of canine parvovirus type 2c (CPV-2c) in cell cultures from South American dogs.