DistSNE: Distributed computing and online visualization of DNA methylation-based central nervous system tumor classification

The current state-of-the-art analysis of central nervous system (CNS) tumors through DNA methylation profiling relies on the tumor classifier developed by Capper and colleagues, which centrally harnesses DNA methylation data provided by users. Here, we present a distributed-computing-based approach for CNS tumor classification that achieves a comparable performance to centralized systems while safeguarding privacy. We utilize the t-distributed neighborhood embedding (t-SNE) model for dimensionality reduction and visualization of tumor classification results in two-dimensional graphs in a distributed approach across multiple sites (DistSNE). DistSNE provides an intuitive web interface (https://gin-tsne.med.uni-giessen.de) for user-friendly local data management and federated methylome-based tumor classification calculations for multiple collaborators in a DataSHIELD environment. The freely accessible web interface supports convenient data upload, result review, and summary report generation. Importantly, increasing sample size as achieved through distributed access to additional datasets allows DistSNE to improve cluster analysis and enhance predictive power. Collectively, DistSNE enables a simple and fast classification of CNS tumors using large-scale methylation data from distributed sources, while maintaining the privacy and allowing easy and flexible network expansion to other institutes. This approach holds great potential for advancing human brain tumor classification and fostering collaborative precision medicine in neuro-oncology.

Alpha-1-antitrypsin-deficiency is associated with lower cardiovascular risk: an approach based on federated learning

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is an inflammatory multisystemic disease caused by environmental exposures and/or genetic factors. Inherited alpha-1-antitrypsin deficiency (AATD) is one of the best recognized genetic factors increasing the risk for an early onset COPD with emphysema. The aim of this study was to gain a better understanding of the associations between comorbidities and specific biomarkers in COPD patients with and without AATD to enable future investigations aimed, for example, at identifying risk factors or improving care.

METHODS

We focused on cardiovascular comorbidities, blood high sensitivity troponin (hs-troponin) and lipid profiles in COPD patients with and without AATD. We used clinical data from six German University Medical Centres of the MIRACUM (Medical Informatics Initiative in Research and Medicine) consortium. The codes for the international classification of diseases (ICD) were used for COPD as a main diagnosis and for comorbidities and blood laboratory data were obtained. Data analyses were based on the DataSHIELD framework.

RESULTS

Out of 112,852 visits complete information was available for 43,057 COPD patients. According to our findings, 746 patients with AATD (1.73%) showed significantly lower total blood cholesterol levels and less cardiovascular comorbidities than non-AATD COPD patients. Moreover, after adjusting for the confounder factors, such as age, gender, and nicotine abuse, we confirmed that hs-troponin is a suitable predictor of overall mortality in COPD patients. The comorbidities associated with AATD in the current study differ from other studies, which may reflect geographic and population-based differences as well as the heterogeneous characteristics of AATD.

CONCLUSION

The concept of MIRACUM is suitable for the analysis of a large healthcare database. This study provided evidence that COPD patients with AATD have a lower cardiovascular risk and revealed that hs-troponin is a predictor for hospital mortality in individuals with COPD.

Awareness of Thyroid Disorders among Nepalese Women: A Cross-Sectional Study

Background Thyroid disorders are emerging public health issues. Clients' awareness is crucial for prevention, early diagnosis, and treatment of the thyroid disorders. Studies, assessing knowledge on thyroid disorders among Nepalese population, is lacking. Objective To assess the awareness of thyroid disorders among women, a susceptible subgroup, and find the correlates of poor knowledge. Method A cross-sectional study was conducted among 423 women at the gynecological outpatient department of Tribhuvan University Teaching Hospital. Eighteen-item scale, with a Cronbach's Alpha of 0.913, was developed to assess participant's knowledge on various constructs of thyroid disorder. A linear regression model with Bootstrap approach was used to identify the predictors of the total knowledge score. Result The mean (±SD) age of the participant was 29.2 ± 7.0 years. About 49% of the women had inadequate knowledge, defined at or below the mean cumulative knowledge score. In linear regression, the total knowledge score was significantly lower among participants who were Janajati (β=-2.87, BCa 95%CI=-4.61, -1.11), illiterate (β=- 6.37, BCa 95%CI =-9.14, -3.21), and low income (β=-3.76, BCa 95%CI=-5.68, -1.83). Likewise, a university education (β=5.94, BCa 95%CI=3.50, 8.26), working status (β=4.04, BCa 95%CI=2.19, 5.81), urban residence (β=2.06, BCa 95%CI=0.02, 3.96) and family history (β=2.20, BCa 95%CI=0.71, 3.63) of thyroid disorder predicted higher knowledge score. Conclusion This study identified a poor level of knowledge on thyroid disorders among Nepali women and thus proposes them to be an important subgroup for an intervention or policy aimed at promoting awarenessof thyroid disorders. The findings also warrant increased awareness among these population through hospital and communitybased behavior change communication campaigns.

Discovery of a Potent and Orally Bioavailable Cyclophilin Inhibitor Derived from the Sanglifehrin Macrocycle

Cyclophilins are a family of peptidyl-prolyl isomerases that are implicated in a wide range of diseases including hepatitis C. Our aim was to discover through total synthesis an orally bioavailable, non-immunosuppressive cyclophilin (Cyp) inhibitor with potent anti-hepatitis C virus (HCV) activity that could serve as part of an all oral antiviral combination therapy. An initial lead 2 derived from the sanglifehrin A macrocycle was optimized using structure based design to produce a potent and orally bioavailable inhibitor 3. The macrocycle ring size was reduced by one atom, and an internal hydrogen bond drove improved permeability and drug-like properties. 3 demonstrates potent Cyp inhibition ( K_d = 5 nM), potent anti-HCV 2a activity (EC₅₀ = 98 nM), and high oral bioavailability in rat (100%) and dog (55%). The synthetic accessibility and properties of 3 support its potential as an anti-HCV agent and for interrogating the role of Cyp inhibition in a variety of diseases.

Discovery and Characterization of (R)-6-Neopentyl-2-(pyridin-2-ylmethoxy)-6,7-dihydropyrimido[2,1-c][1,4]oxazin-4(9H)-one (PF-06462894), an Alkyne-Lacking Metabotropic Glutamate Receptor 5 Negative Allosteric Modulator Profiled in both Rat and Nonhuman Primates

We previously observed a cutaneous type IV immune response in nonhuman primates (NHP) with the mGlu₅ negative allosteric modulator (NAM) 7. To determine if this adverse event was chemotype- or mechanism-based, we evaluated a distinct series of mGlu₅ NAMs. Increasing the sp³ character of high-throughput screening hit 40 afforded a novel morpholinopyrimidone mGlu₅ NAM series. Its prototype, (R)-6-neopentyl-2-(pyridin-2-ylmethoxy)-6,7-dihydropyrimido[2,1-c][1,4]oxazin-4(9H)-one (PF-06462894, 8), possessed favorable properties and a predicted low clinical dose (2 mg twice daily). Compound 8 did not show any evidence of immune activation in a mouse drug allergy model. Additionally, plasma samples from toxicology studies confirmed that 8 did not form any reactive metabolites. However, 8 caused the identical microscopic skin lesions in NHPs found with 7, albeit with lower severity. Holistically, this work supports the hypothesis that this unique toxicity may be mechanism-based although additional work is required to confirm this and determine clinical relevance.

Comparison of success rate of arterio-venous fistula in patients with diabetes vs non-diabetes

Introduction and objective: Definition of chronic renal disease is based on the presence of kidney damage or glomerular filtration rate (GFR 60 ml/min per 1.73 m2) for 3 months, irrespective of cause[1]. Once they are diagnosed as CKD, they are kept either on hemodialysis or peritoneal dialysis or patient undergo renal transplant.[2,3] With this research we may prove that even in a similar circumstances failure rate of AVF is more in diabetes patient.Materials and Methods: Total 50 patients of either gender were taken in this study. Inclusion criteria: CRF with GFR <30ml/min. Arterial diameter >1.5mm and venous diameter >2mm. Preoperative radial artery blood flow >30cm/min. Exclusion criteria: arterial diameter <1.5mm venous diameter <2mm.Written consent was taken from the patient. After preoperative workup surgery was done by 1st author. Arterio-venous fistula was scanned by color Doppler imaging after 4 weeks.Result: There were 31[62%] male, 19[38%] female. Mean age of patients was 55.8 years. 18[36%] were dialysis dependent. Cause of renal failure were diabetes 16(32%), unknown 15(30%), glomerulonephritis 8[16%] and obstructive uropathy 3[6%]. Mean internal diameter of radial artery was 1.91mm [1.5-2.6] and cephalic vein 2.57mm [1.9-3.2].7 patients had swelling of arm, 5 patients has surgical site infections and 15 patients had primary failure; 11 were from diabetic group and 4 from non-diabetic group. Mean duration of surgery was 60.95 minutes [50-75]. Average preoperative velocity in radial artery was 32.94[30-39]cm/sec. Average flow of blood at the end of 4 weeks was 461.42ml/min [0-654]. Between two groups failure rate was significantly high in diabetic patients [p = 0.02]. Failure rate was significantly higher in patients with diabetes more than 10 years [p=0.01].Conclusion: Failure rate of arterio-venous fistula is significantly high in diabetic patients.

Factors Determining Availability, Utilization and Retention of Child Health Card in Western Nepal

BACKGROUND

The immunization card is revised with addition of general information about child health and is later called as child health card. This card is a tool used by Health Management Information System in Nepal. It is important for tracking the records of immunization. Aim is to identify the factors determining the availability, utilization and retention of the child health card in Western Nepal.

METHODS

A cross sectional study was conducted among mothers having children < 24 months old from Gorkha (Western Hill) and Nawalparasi (Western Terai) districts. The sample size for the study was 600 and systematic random sampling was used to select the mothers having less than 24 months old children. Data entry and analysis was done by using SPSS. Qualitative data was analyzed by making matrix.

RESULTS

The average age of respondents was 24 years. The majority of respondents have gained higher level education. Retention of the card was found to be 82.2%. 90.3% retention was seen among 0-12 months children age group whereas it was 74 % among12 to 24 months age group. The reasons for less retention were torn by the child/played by child (54.6%) followed by lack of proper place,unaware about importance and poor quality of card.The new child health cards were insufficient, compelling use of both new and old cards which created problem in consistency. Regarding utilization of child health card, it was found to be used for birth registration and for further studies in abroad.

CONCLUSIONS

The areas of utilization of child health card should be broadened so that the retention of card can be increased. The main reasons for less retention of the card are torn by children and lack of the proper place.

The discovery and characterization of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor potentiator N-{(3S,4S)-4-[4-(5-cyano-2-thienyl)phenoxy]tetrahydrofuran-3-yl}propane-2-sulfonamide (PF-04958242)

A unique tetrahydrofuran ether class of highly potent α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor potentiators has been identified using rational and structure-based drug design. An acyclic lead compound, containing an ether-linked isopropylsulfonamide and biphenyl group, was pharmacologically augmented by converting it to a conformationally constrained tetrahydrofuran to improve key interactions with the human GluA2 ligand-binding domain. Subsequent replacement of the distal phenyl motif with 2-cyanothiophene to enhance its potency, selectivity, and metabolic stability afforded N-{(3S,4S)-4-[4-(5-cyano-2-thienyl)phenoxy]tetrahydrofuran-3-yl}propane-2-sulfonamide (PF-04958242, 3), whose preclinical characterization suggests an adequate therapeutic index, aided by low projected human oral pharmacokinetic variability, for clinical studies exploring its ability to attenuate cognitive deficits in patients with schizophrenia.

Discovery of β-D-2'-deoxy-2'-α-fluoro-4'-α-cyano-5-aza-7,9-dideaza adenosine as a potent nucleoside inhibitor of respiratory syncytial virus with excellent selectivity over mitochondrial RNA and DNA polymerases

Novel 4'-substituted β-d-2'-deoxy-2'-α-fluoro (2'd2'F) nucleoside inhibitors of respiratory syncytial virus (RSV) are reported. The introduction of 4'-substitution onto 2'd2'F nucleoside analogs resulted in compounds demonstrating potent cell based RSV inhibition, improved inhibition of the RSV polymerase by the nucleoside triphosphate metabolites, and enhanced selectivity over incorporation by mitochondrial RNA and DNA polymerases. Selectivity over the mitochondrial polymerases was found to be extremely sensitive to the specific 4'-substitution and not readily predictable. Combining the most potent and selective 4'-groups from N-nucleoside analogs onto a 2'd2'F C-nucleoside analog resulted in the identification of β-D-2'-deoxy-2'-α-fluoro-4'-α-cyano-5-aza-7,9-dideaza adenosine as a promising nucleoside lead for RSV.

Need and importance of health protection training in Nepal

By investing in health protection, the health of the nation can be safeguarded from future threats of uncontrolled infectious disease epidemics and disasters. DOI: http://dx.doi.org/10.3126/nje.v5i1.12373

The design and synthesis of indazole and pyrazolopyridine based glucokinase activators for the treatment of type 2 diabetes mellitus

Glucokinase activators represent a promising potential treatment for patients with Type 2 diabetes. Herein, we report the identification and optimization of a series of novel indazole and pyrazolopyridine based activators leading to the identification of 4-(6-(azetidine-1-carbonyl)-5-fluoropyridin-3-yloxy)-2-ethyl-N-(5-methylpyrazin-2-yl)-2H-indazole-6-carboxamide (42) as a potent activator with favorable preclinical pharmacokinetic properties and in vivo efficacy.

Retroperitoneal Hamartoma: A Rare Entity

Retroperitoneal hamartoma in adult is an extremely rare entity. Here we report a case of 23-years-old lady who presented with alarge retroperitoneal mass and abdominal pain. The mass was surgically removed and the diagnosis of hamartoma was made on histological findings. Keywords: hamartoma malformative tumor, retroperitoneal.

Retroperitoneal hamartoma: a rare entity

Retroperitoneal hamartoma in adult is an extremely rare entity. Here we report a case of 23-years-old lady who presented with a large retroperitoneal mass and abdominal pain. The mass was surgically removed and the diagnosis of hamartoma was made on histological findings.

Application of the bicyclo[1.1.1]pentane motif as a nonclassical phenyl ring bioisostere in the design of a potent and orally active γ-secretase inhibitor

Replacement of the central, para-substituted fluorophenyl ring in the γ-secretase inhibitor 1 (BMS-708,163) with the bicyclo[1.1.1]pentane motif led to the discovery of compound 3, an equipotent enzyme inhibitor with significant improvements in passive permeability and aqueous solubility. The modified biopharmaceutical properties of 3 translated into excellent oral absorption characteristics (~4-fold ↑ C(max) and AUC values relative to 1) in a mouse model of γ-secretase inhibition. In addition, SAR studies into other fluorophenyl replacements indicate the intrinsic advantages of the bicyclo[1.1.1]pentane moiety over conventional phenyl ring replacements with respect to achieving an optimal balance of properties (e.g., γ-secretase inhibition, aqueous solubility/permeability, in vitro metabolic stability). Overall, this work enhances the scope of the [1.1.1]-bicycle beyond that of a mere "spacer" unit and presents a compelling case for its broader application as a phenyl group replacement in scenarios where the aromatic ring count impacts physicochemical parameters and overall drug-likeness.

Cycloaddition of Cyclohexa-2,4-dienones, Ring-Closing Metathesis, and Photochemical Reactions: A Common Stereoselective Approach to Duprezianane, Polyquinane and Sterpurane Frameworks

A novel approach to three different types of carbocyclic frameworks belonging to dupreziananes, sterpuranes, and polyquinanes from simple aromatic precursors has been presented. Cycloaddition of appropriately appended cyclohexa-2,4-dienones with acyclic dienes gave bridged bicyclic octanes suitably disposed with olefinic chains, which upon ring-closing metathesis led to functionalized tricyclo[5.2.2.0(1,5)]undecanes related to dupreziananes. Photochemical sigmatropic 1,2- and 1,3-acyl shifts in tricyclo[5.2.2.0(1,5)] undecanes upon triplet and singlet excitation provided stereoselective routes to sterpurane and polyquinane frameworks.

Molecular distortions and chemical bonding of a large pi-conjugated molecule on a metal surface

Normal incidence x-ray standing wave experiments and density functional theory reveal that 3,4,9,10-perylene-tetracarboxylic-dianhydride chemisorbs on Ag(111) in a nonplanar but vertically distorted configuration. The carboxylic O atoms are 0.18 +/- 0.03 angstroms closer to the surface than the perylene core. The distortion is related to weak, local bonds between carboxylic O atoms and the Ag surface which are coupled--through charge transfer into the former lowest unoccupied molecular orbital--to the primary, extended chemisorption bond via the perylene skeleton.