Design of Antigen-Specific Antibody CDRH3 Sequences Using AI and Germline-Based Templates.

Antibody-antigen specificity is engendered and refined through a number of complex B cell processes, including germline gene recombination and somatic hypermutation. Here, we present an AI-based technology for de novo generation of antigen-specific antibody CDRH3 sequences using germline-based templates, and validate this technology through the generation of antibodies against SARS-CoV-2. AI-based processes that mimic the outcome, but bypass the complexity of natural antibody generation, can be efficient and effective alternatives to traditional experimental approaches for antibody discovery.

The Predisposition for Type 2 Diabetes Mellitus and Metabolic Syndrome.

Type 2 diabetes mellitus (T2DM) and metabolic syndrome (MetS) are diseases caused by the interaction of genetic and non-genetic factors. Therefore, the aim of our study was to investigate the association between six common genetic polymorphisms and T2DM and MetS in males. A total of 120 T2DM, 75 MetS, and 120 healthy controls (HC) were included in the study. ACE ID, eNOS 4a/b, ATR1 A1166C, OXTR (A>G), SOD1 +35A/C, CAT-21A/T gene polymorphisms were genotyped by PCR or PCR-RFLP techniques. T2DM was diagnosed at an earlier age compared to MetS (54 vs 55 years old, p=0.0003) and the difference was greater in carriers of the OXTR G allele (54 vs 56 years old, p=0.0002) or both OXTR G and eNOS b alleles (54 vs 56, p=0.00016). The SOD1 AA genotype (O.R.=0.11, p=0.0006) and the presence of both ACE I and OXTR1 A (O.R.=0.39, p=0.0005) alleles revealed to be protective for T2DM. SOD1 AA and AC genotypes were protective factors for triglyceride (p=0.0002 and p=0.0005, respectively) and HDL cholesterol (p=0.0002 and p=0.0004, respectively) levels in T2DM patients. ACE DD was identified more frequently in hypertensive T2DM patients (O.R.=3.77, p=0.0005) and in those who reported drinking alcohol (p=0.0001) comparing to HC and T2DM patients who did not drink alcohol, respectively. We observed that T2DM patients who reported drinking alcohol had an increased frequency of ACE DD and eNOS bb (p<0.0001), or ACE DD and OXTR G (p<0.0001) compared to non-drinkers. No gene polymorphisms were associated with MetS.

The outcomes of open anterior component separation versus posterior component separation with transversus abdominis release for complex incisional hernias: a systematic review and meta-analysis.

PURPOSE: The main objective was to assess the prevalence of hernia recurrence, wound complications (surgical site infections [SSI], seroma and hematoma) and mortality after anterior component separation (ACS) and posterior component separation via transversus abdominis muscle release (PCSTAR) in patients with complex incisional hernias. The so-called complex IH is a serious medical and societal challenge due to its direct and indirect costs; it is also hampered by the use of different surgical techniques, different type of meshes, and different results heterogeneously reported and interpreted. According to actual data, the best approach seems to be a mesh reinforcement component separation procedure augmented or not with an adjuvant technique (preoperative progressive pneumoperitoneum and/or Botulin toxin type A infiltration). METHODS: A systematic search of four databases (MEDLINE, PubMed, Web of Science, and Google Scholars) was conducted to identify studies reporting on outcomes of component separation techniques and which were published before December 2021. A systematic review and a meta-analysis of postoperative outcomes were performed. RESULTS: Nineteen studies including 3412 patients (1709 with ACS and 1703 with PCSTAR) were selected. Pooled hernia recurrence rate after a minimum 1-year follow-up was evaluated at 5.15% (odds ratio [OR] 0.68; 95% confidence interval [CI] 0.5-0.9; p = 0.0175). Pooled surgical site infection rate was 10.6% (OR 1.32; 95% CI 1.06-1.65; p = 0.0119). Seroma and hematoma were estimated at 9.75% (OR 1.93; 95% CI 1.52-2.44; p = 0.0001) and 3.83% (OR 1.81; 95% CI 1.26-2.61; p = 0.0012), respectively. ACS was associated with increased wound morbidity, seroma and hematoma. PCSTAR displayed higher recurrence rate (4.27% vs 6.11%). CONCLUSIONS: PCSTAR was superior to ACS in terms of wound morbidity, surgical site infections, seroma and hematoma incidence. The procedure should be further evaluated in comparative head-to-head randomized controlled trials.

Truncal function after abdominal wall reconstruction via transversus abdominis muscle release (TAR) for large incisional hernias: a prospective case-control study.

BACKGROUND: Data about abdominal wall function in patients with incisional hernias (IH) are limited. Abdominal Wall Reconstruction (AWR) could be beneficial for the improvement of this function. The goal of the study was to evaluate if the abdominal wall function was restored after transversus abdominis muscle release (TAR). METHODS: We performed a prospective case-control study of 59 patients with IH equal or larger than 10 cm in their width undergoing AWR via TAR with mesh reinforcement and complete linea alba restoration. With two simple physical tests-Trunk Raising (TR) and Double Leg Lowering (DLL), we clinically assessed, preoperatively, 1 month and 1 year postoperatively the functionality of the abdominal wall (flexion). Patients were compared with a control group (n = 57) with an intact abdominal wall undergoing visceral surgery through a midline laparotomy. RESULTS: There were no differences between the groups in terms of sex and mean age. In the study group, TR demonstrated an increase from 1.93 preoperatively to 2.44 at 1 month and 4.27, respectively, at 1 year postoperatively (p < 0.001). DLL was improved from 2.067 to 4.37 at 1 year postoperatively (p = 0.016). In the control group, surgery resulted in a decrease of truncal flexion. At 1 year postoperatively, the abdominal wall function for study group patients was almost identical with that the functionality of the control group featuring an intact abdominal wall (TR 4.26 vs 4.33 p = 0.532; DLL 4.42 vs 4.21 p = 0.193). CONCLUSION: AWR via TAR for large IH specifically improved long-term abdominal wall muscular function.

Thresholding Segmentation Errors and Uncertainty with Patient-Specific Geometries.

Computer simulations provide virtual hands-on experience when actual hands-on experience is not possible. To use these simulations in medical science, they need to be able to predict the behavior of actual processes with actual patient-specific geometries. Many uncertainties enter in the process of developing these simulations, starting with creating the geometry. The actual patient-specific geometry is often complex and hard to process. Usually, simplifications to the geometry are introduced in exchange for faster results. However, when simplified, these simulations can no longer be considered patient-specific as they do not represent the actual patient they come from. The ultimate goal is to keep the geometries truly patient-specific without any simplification. However, even without simplifications, the patient-specific geometries are based on medical imaging modalities and consequent use of numerical algorithms to create and process the 3D surface. Multiple users are asked to process medical images of a complex geometry. Their resulting geometries are used to assess how the user's choices determine the resulting dimensions of the 3D model. It is shown that the resulting geometry heavily depends on user's choices.

[Status of the availability and use of next generation sequencing (NGS) in bladder cancer-a questionnaire within the uropathology working group]. / Status der Verfügbarkeit und Anwendung von "next generation sequencing" (NGS) beim Harnblasenkarzinom ­ eine Umfrage in der Arbeitsgemeinschaft Uropathologie.

BACKGROUND: Technical advancement and availability of high-throughput analysis has advanced molecular subtyping of most cancers. Thus, new possibilities for precision oncology have emerged. AIM: Therefore, we aimed to collect data regarding availability and use of next generation sequencing (NGS) for urothelial cancer within the uropathology working group of the German Society of Pathology. METHODS: We collected data by questionnaires and additionally asked for sequencing results of bladder cancers in the participating institutions. RESULTS: A total of 13 university-affiliated institutes of pathology took part in the survey. All university institutes offer NGS-based molecular panel diagnostics and provide panels covering between 15 and 170 genes. Altogether, only 20 bladder cancers were sequenced in routine diagnostics and for 10 cancers potential targeted treatment options were available. DISCUSSION: So far, despite availability of NGS diagnostics at university institutes of pathology, only few bladder cancer samples have been sequenced. Based on current data from the molecular subtyping of bladder cancers, we recommend a step-by-step protocol with basic immunohistochemistry analysis and subsequent subtype-dependent analyses, e.g., alterations of the fibroblast growth factor receptors (FGFR) or comprehensive gene panel analyses.

Association between varicose veins anatomical pattern and procedural complications following endovascular laser photothermolysis for chronic venous insufficiency.

We sought to assess clinical characteristics and pattern of collateral network involvement associated with development of truncal (systematized) versus diffuse/non-truncal (non-systematized) varicose veins (VVs) in patients undergoing endovascular laser photothermolysis for chronic venous insufficiency (CVI). Secondly, we aimed to assess whether the type of VVs influenced the procedural complications of endovascular laser therapy. A total of 508 patients with hydrostatic VVs of the lower limbs who underwent endovenous laser treatment were included, out of which 84.1% (n=427) had truncal VVs (group 1) and 15.9% (n=81) had diffuse (non-systematized) VVs (group 2). Patients with truncal varices were significantly older (47.50±12.80 vs 43.15±11.75 years, P=0.004) and those with associated connective tissue disorders were more prone to present diffuse VVs (P=0.004). Patients in group 1 presented a significantly higher number of Cockett 1 (P=0.0017), Cockett 2 (P=0.0137), Sherman (P<0.0001), and Hunter (P=0.0011) perforator veins compared to group 2, who presented a higher incidence of Kosinski perforators (P<0.0001). There were no significant differences regarding postoperative complications: thrombophlebitis (P=0.773), local inflammation (P=0.471), pain (P=0.243), paresthesia (P=1.000), or burning sensation (P=0.632). Patients with more advanced CEAP (clinical, etiologic, anatomic, pathophysiologic) classes were older (P<0.0001), more were males (39.05 vs 27.77%, P=0.0084), more were prone to present ulcers (P<0.0001) and local hyperthermia (P=0.019), and presented for endovenous phlebectomy after a longer time from symptom onset. In patients with CVI, systematized VVs were associated with a more severe clinical status and a distinct anatomical pattern of perforators network compared to non-systematized VVs, which is more common in advanced stages.

Association between varicose veins anatomical pattern and procedural complications following endovascular laser photothermolysis for chronic venous insufficiency

We sought to assess clinical characteristics and pattern of collateral network involvement associated with development of truncal (systematized) versus diffuse/non-truncal (non-systematized) varicose veins (VVs) in patients undergoing endovascular laser photothermolysis for chronic venous insufficiency (CVI). Secondly, we aimed to assess whether the type of VVs influenced the procedural complications of endovascular laser therapy. A total of 508 patients with hydrostatic VVs of the lower limbs who underwent endovenous laser treatment were included, out of which 84.1% (n=427) had truncal VVs (group 1) and 15.9% (n=81) had diffuse (non-systematized) VVs (group 2). Patients with truncal varices were significantly older (47.50±12.80 vs 43.15±11.75 years, P=0.004) and those with associated connective tissue disorders were more prone to present diffuse VVs (P=0.004). Patients in group 1 presented a significantly higher number of Cockett 1 (P=0.0017), Cockett 2 (P=0.0137), Sherman (P<0.0001), and Hunter (P=0.0011) perforator veins compared to group 2, who presented a higher incidence of Kosinski perforators (P<0.0001). There were no significant differences regarding postoperative complications: thrombophlebitis (P=0.773), local inflammation (P=0.471), pain (P=0.243), paresthesia (P=1.000), or burning sensation (P=0.632). Patients with more advanced CEAP (clinical, etiologic, anatomic, pathophysiologic) classes were older (P<0.0001), more were males (39.05 vs 27.77%, P=0.0084), more were prone to present ulcers (P<0.0001) and local hyperthermia (P=0.019), and presented for endovenous phlebectomy after a longer time from symptom onset. In patients with CVI, systematized VVs were associated with a more severe clinical status and a distinct anatomical pattern of perforators network compared to non-systematized VVs, which is more common in advanced stages.

[Development and treatment of localized/systemic BCGitis : Retrospective studies in direct comparison to mitomycin C]. / Zur urogenitalen Klinik der lokalisierten/systemischen BCGitis : Retrospektive Untersuchungen im direkten Vergleich zu Mitomycin C.

Adjuvant therapy with different bacillus Calmette-Guérin (BCG) preparations is a well-established guideline-endorsed treatment for nonmuscle invasive bladder cancer (NMIBC). Our observational study demonstrates equality between BCG and mitomycin C (MMC) treatment based on the oncological outcome. However, there were significant toxicity differences with higher rates in the BCG treatment group. The potential adverse effects of BCG in terms of a BCGitis are controversially discussed regarding their occurrence. As such, we sought to retrospectively evaluate the incidence in 106 consecutive patients. The BCG group demonstrated minor adverse effects in 78.4% and major adverse effects in 43.3%-partially coincident. Moreover, the parallel MMC group showed in 34.7% respectively 1.4% adverse events-as expected distinctly lower. In the context of this clinical discussion, we refer to alternative treatment concepts. Our data show a high clinical relevance of the patient's primary comorbidity.

Rapid and sensitive detection of neuron specific enolase with a polydopamine coated plasmonic chip utilizing a rear-side coupling method.

A rapid and sensitive detection of a cancer marker, neuron specific enolase (NSE), is demonstrated by using a disposable silver plasmonic chip functionalized with a mussel-inspired polydopamine (PDA) coating. A plasmonic chip consisting of a diffraction grating coated with a silver thin film is used for the excitation of propagating surface plasmon resonance through a rear-side grating coupling method. Simple and quick bio-functionalization of the sensor surface is performed by PDA coating which requires 20 min for deposition, and allows direct attachment of the capture antibody without using any coupling agents. A fluorescence based sandwich immunoassay is used for the detection of NSE by utilizing surface plasmon enhanced fluorescence (SPF) spectroscopy. The developed biosensor scheme provides approximately linear sensor responses for the sample containing NSE with the concentration around the clinically important value (12 ng mL-1) in both buffer and diluted human serum (25 vol% to a buffer solution). The detection limit for NSE is 0.5 ng mL-1 (11 pM) and 1.4 ng mL-1 (30 pM) in a buffer solution and diluted human serum, respectively. The presented biosensor scheme requires a small amount of the sample down to 10 µL in human serum and a short incubation time (15 min) of the sample solution containing NSE, enabling less invasive and rapid detection of NSE. This is the first example of the sensitive sandwich immunoassay demonstrated by using a plasmonic chip for the measurement of the sample dissolved in a complex medium with a rear side coupling method, which progresses the universal use of the SPF biosensors with a disposable plasmonic chip.

[Incidental undifferentiated carcinoma of the prostate: A case with unusual diagnosis]. / Inzidentelles undifferenziertes Karzinom der Prostata : Ein Fall mit überraschender Wendung.

A 69-year-old man presented with an incidental undifferentiated carcinoma of the prostate. Ten years ago the patient had clinical stage I seminoma of the right testis with adjuvant radiotherapy. Follow-up care was without pathological findings. Staging examinations did not show metastatic disease. After radical prostatectomy with pelvic lymphadenectomy, the histological examination revealed a metastatic seminoma in the prostate. Therefore, the diagnosis was a late relapse in an extremely rare location. So far only four other reports describe testicular seminoma with metastases to the prostate.

Cardiovascular MRI predicts 5-year adverse clinical outcome in heart transplant recipients.

Imaging recommendations for the follow-up of heart transplant recipients (HTRs) lack evidence justifying their prognostic value. Cardiovascular magnetic resonance imaging (CMRI) can characterize heart structure and function and has prognostic value in many myocardial diseases. We hypothesized that CMRI evaluation of cardiac allografts would predict adverse events. We performed CMRI on 60 HTRs evaluating biventricular size, function and myocardial scar. We performed survival analysis to identify independent predictors of cardiovascular (CV) death or hospitalization. Participants had a mean age of 51 ± 14 years, mean graft age of 3.5 years (±4) and 75% are male. Median follow-up time was 4.9 years with 22 CV hospitalizations and 7 CV deaths. A multivariable survival analysis of imaging and clinical variables identified myocardial scar (hazard ratio [HR] of 10.7, p = 0.005), right ventricular end- diastolic volume index (RVEDVI; 1.1/mL/m(2) , p = 0.001), graft age (HR = 1.2/year, p = 0.004) and previous allograft rejection (HR = 4.4, p = 0.006) as predictive of time to CV death or hospitalization. CMRI-derived myocardial scar and RVEDVI are independently associated with CV outcomes in HTRs.

Neuronal spike timing adaptation described with a fractional leaky integrate-and-fire model.

The voltage trace of neuronal activities can follow multiple timescale dynamics that arise from correlated membrane conductances. Such processes can result in power-law behavior in which the membrane voltage cannot be characterized with a single time constant. The emergent effect of these membrane correlations is a non-Markovian process that can be modeled with a fractional derivative. A fractional derivative is a non-local process in which the value of the variable is determined by integrating a temporal weighted voltage trace, also called the memory trace. Here we developed and analyzed a fractional leaky integrate-and-fire model in which the exponent of the fractional derivative can vary from 0 to 1, with 1 representing the normal derivative. As the exponent of the fractional derivative decreases, the weights of the voltage trace increase. Thus, the value of the voltage is increasingly correlated with the trajectory of the voltage in the past. By varying only the fractional exponent, our model can reproduce upward and downward spike adaptations found experimentally in neocortical pyramidal cells and tectal neurons in vitro. The model also produces spikes with longer first-spike latency and high inter-spike variability with power-law distribution. We further analyze spike adaptation and the responses to noisy and oscillatory input. The fractional model generates reliable spike patterns in response to noisy input. Overall, the spiking activity of the fractional leaky integrate-and-fire model deviates from the spiking activity of the Markovian model and reflects the temporal accumulated intrinsic membrane dynamics that affect the response of the neuron to external stimulation.

Computational modeling of diffusion in the cerebellum.

Diffusion is a major transport mechanism in living organisms. In the cerebellum, diffusion is responsible for the propagation of molecular signaling involved in synaptic plasticity and metabolism, both intracellularly and extracellularly. In this chapter, we present an overview of the cerebellar structure and function. We then discuss the types of diffusion processes present in the cerebellum and their biological importance. We particularly emphasize the differences between extracellular and intracellular diffusion and the presence of tortuosity and anomalous diffusion in different parts of the cerebellar cortex. We provide a mathematical introduction to diffusion and a conceptual overview of various computational modeling techniques. We discuss their scope and their limit of application. Although our focus is the cerebellum, we have aimed at presenting the biological and mathematical foundations as general as possible to be applicable to any other area in biology in which diffusion is of importance.

Rapid detection of human torque teno viruses using high-resolution melting analysis.

Torque teno viruses (TTVs) are recently discovered DNA viruses, with heterogeneous genomes, highly prevalent in populations worldwide. The species that infect humans are Torque teno virus (TTV), Torque teno midi virus (TTMDV) and Torque teno mini virus (TTMV). High-resolution melting analysis (HRMA) is a sensitive and effective method for genotyping and mutation scanning. Up to now, HRMA has not been utilized for detection of TTVs. The aim of this study was to asses if HRMA is suitable for detecting TTVs variants. DNA was extracted from the blood and saliva of 13 healthy subjects for method optimization. Additionally, saliva samples from 100 healthy individuals were collected for estimating the TTVs' prevalence. Viral DNA was amplified by heminested polymerase chain reaction (PCR). Second round amplicons were used for the HRMA. The samples were analyzed using two fluorescent dyes, SYBR (®) Green I and EvaGreen®. The prevalence values for TTV, TTMDV and TTMV were 71.0, 31.0 and 54.0%, respectively. The three major melting curve patterns corresponding to TTV, TTMDV and TTMV on HRMA can be easily distinguished regardless of kit used. Our results showed that HRMA is a rapid and efficient method of detecting human TTVs.

Analysis of several BRCA1 and BRCA2 mutations in a hospital-based series of unselected breast cancer cases.

BACKGROUND: The distribution of BRCA mutations varies significantly between populations. The spectrum of BRCA1 and BRCA2 mutations in breast cancers in the Romanian population is incompletely known. The aim of the present study is to investigate the presence of nine BRCA mutations in patients with breast cancer identified in a surgical clinic from Bucharest. METHODS: Unrelated women diagnosed with breast cancer from Coltea Hospital (n=114) and healthy controls (n = 150) were selected for this study. Seven mutations in BRCA1 (185delAG, 5382insC, 943ins10, E1250X, 1294del40, E1373X, R1443X) and two in BRCA2 (IVS16-2A4G and 6174delT) were tested using PCR based protocols. In addition, the presence of BRCA1 185delAG, BRCA1 5382insC, BRCA2 6174delT mutations were tested with a post amplification mutation detection system, based on the ELISA method. RESULTS: Two patients with sporadic breast cancer (2%) and one patient with family history of the disease (7.14%) have the BRCA1 5382insC mutation. No other mutation was detected in patient and control groups. The mutations were not present in the control lot. CONCLUSIONS: Our results indicate that BRCA1 5382insC is a common mutation in Romanian women with breast cancer (3 114).

FRACTIONAL INTEGRATION TOOLBOX.

The problems formulated in the fractional calculus framework often require numerical fractional integration/differentiation of large data sets. Several existing fractional control toolboxes are capable of performing fractional calculus operations, however, none of them can efficiently perform numerical integration on multiple large data sequences. We developed a Fractional Integration Toolbox (FIT), which efficiently performs fractional numerical integration/differentiation of the Riemann-Liouville type on large data sequences. The toolbox allows parallelization and is designed to be deployed on both CPU and GPU platforms.

Gallstone disease in young population: incidence, complications, therapeutic approach.

OBJECTIVE: The purpose of this study is to highlight the high incidence of gallstones and the etiology in young people, as well as the fact that the onset is associated with complications: i.e. acute pancreatitis, jaundice. MATERIAL AND METHODS: This retrospective study was conducted between January 2007 and February 2012 on patients admitted to the two surgical wards of Pitesti District Hospital and was based on the analysis of observation charts and theatre records. A total of 1905 cholecystectomies were performed, 1023 laparoscopic and 882 classic, respectively. RESULTS: A total of 36 patients aged between 16 and 25 years were included in the study. Laparoscopic cholecystectomy was performed in 34 patients, only two patients being operated by the classical open approach. 6 patients developed postoperative jaundice, which resolved under medical treatment in 3 patients within 3-5 days. The remaining 3 patients underwent endoscopic retrograde cholangiopancreatography (ERCP) 4-5 days postoperatively. CONCLUSIONS: The most important risk factors for gallstones are: age, female gender, pregnancy and obesity. Common complications of gallstones in young people are: duct stones and acute pancreatitis.