Identification of novel inhibitors targeting TIRAP interactions with BTK and PKCδ in inflammation through an in silico approach.

Advanced computational tools focusing on protein-protein interaction (PPI) based drug development is a powerful platform to accelerate the therapeutic development of small lead molecules and repurposed drugs. Toll/interleukin-1 receptor (TIR) domain-containing adapter protein (TIRAP) and its interactions with other proteins in macrophages signalling are crucial components of severe or persistent inflammation. TIRAP activation through Bruton's tyrosine kinase (BTK) and Protein Kinase C delta (PKCδ) is essential for downstream inflammatory signalling. We created homology-based structural models of BTK and PKCδ in MODELLER 9.24. TIRAP interactions with BTK and PKCδ in its non-phosphorylated and phosphorylated states were determined by multiple docking tools including HADDOCK 2.4, pyDockWEB and ClusPro 2.0. Food and Drug Administration (FDA)-approved drugs were virtually screened through Discovery Studio LibDock and Autodock Vina tools to target the common TIR domain residues of TIRAP, which interact with both BTK and PKC at the identified interfacial sites of the complexes. Four FDA-approved drugs were identified and found to have stable interactions over a range of 100 ns MD simulation timescales. These drugs block the interactions of both kinases with TIRAP in silico. Hence, these drugs have the potential to dampen downstream inflammatory signalling and inflammation-mediated disease.

Elective oocyte cryopreservation for age-related fertility decline.

PURPOSE: Women who pursue fertility at an advanced age are increasingly common. Family planning and sexual education have traditionally focused on contraception and prevention of sexually transmitted diseases. A focus should now also be placed on fertility awareness and fertility preservation. This manuscript aims to give an update on the existing evidence around elective oocyte cryopreservation, also highlighting the need for fertility education and evidence-based, individualized counselling. METHODS: A thorough electronic search was performed from the start of databases to March 2020 aiming to summarize the existing evidence around elective egg freezing, the logic behind its use, patient counselling and education, success rates and risks involved, regulation, cost-effectiveness, current status and future perspectives. RESULTS: Clinician-led counselling regarding reproductive aging and fertility preservation is often overlooked. Elective oocyte cryopreservation is not a guarantee of live birth, and the answer regarding cost-effectiveness needs to be individualized. The existing studies on obstetric and perinatal outcomes following the use of egg freezing are, until now, reassuring. Constant monitoring of short-term and long-term outcomes, uniform regulation and evidence-based, individualized counselling is of paramount importance. CONCLUSIONS: Elective oocyte cryopreservation is one of the most controversial aspects of the world of assisted reproduction, and a lot of questions remain unanswered. However, women today do have this option which was not available in the past. Elective oocyte cryopreservation for age-related fertility decline should be incorporated in women's reproductive options to ensure informed decisions and reproductive autonomy.

Anharmonic, dimensionality and size effects in phonon transport (2017J. Phys.: Condens. Matter29 505703).

Corrigendum to 2017J. Phys.: Condens. Matter29505703.

Detection of mutations in the rpoB gene of rifampicin-resistant Mycobacterium tuberculosis strains inhibiting wild type probe hybridization in the MTBDR plus assay by DNA sequencing directly from clinical specimens.

BACKGROUND: The potential of genetic testing for rapid and accurate diagnosis of drug-resistant Mycobacterium tuberculosis strains is vital for efficient treatment and reduction in dissemination. MTBDR plus assays rapidly detect mutations related to drug resistance and wild type sequences allied with susceptibility. Although these methods are promising, the examination of molecular level performance is essential for improved assay result interpretation and continued diagnostic development. Therefore this study aimed to determine novel mutations that were inhibiting wild type probe hybridization in the Line probe assay by DNA sequencing. Using data collected from Line Probe assay (GenoType MTBDRplus assay) the contribution of absent wild type probe hybridization to the detection of rifampicin resistance was assessed via comparison to a reference standard method i.e. DNA sequencing. RESULTS: Sequence analysis of the rpoB gene of 47 MTB resistant strains from clinical specimens showed that 37 had a single mutation, 9 had double mutations and one had triple mutations in the ropB gene. CONCLUSIONS: The absence of wild type probe hybridization without mutation probe hybridization was mainly the result of the failure of mutation probe hybridization and the result of the novel or rare mutations. Additional probes are necessary to be included in the Line probe assay to improve the detection of rifampicin-resistant Mycobacterium tuberculosis strains.

Frequency and degree of inter-trait association of maxillary Non-Metric Dental Crown Traits in the permanent dentitions of two states of India.

Non-metric Dental Crown Traits are a principal source of information in forensic dentistry. However, inadequate data on the prevalence of these traits prompted this study to determine the frequency, sexual dimorphism and degree of inter-trait association in two different populations of India. Dichotomized data on the existence of non-metric features were recorded among individuals from Odisha (n=506) and Kerala (n=536) between 15 to 30 years of age. Cusp of Carabelli is the most common trait to occur (48 %) followed by shovelling of incisors (15%) and Bushman canine (14%). Bushman canine (p=0.045) and Cusp of Carabelli (p = 0.041) were found to be significantly expressed in Odisha and Kerala populations respectively. A strong association between shovelling of central incisor and Bushman canine with a likelihood ratio of 14.041 (p=0.001) was observed. This study will help in characterizing the Indian dentition and post-mortem dental profiling.

Tunable Thermal Transport Characteristics of Nanocomposites.

We present a study of tunable thermal transport characteristics of nanocomposites by employing a combination of a full-scale semi-ab inito approach and a generalised and extended modification of the effective medium theory. Investigations are made for planar superlattices (PSLs) and nanodot superlattices (NDSLs) constructed from isotropic conductivity covalent materials Si and Ge, and NDSLs constructed from anisotropic conductivity covalent-van der Waals materials MoS 2 and WS 2 . It is found that difference in the conductivities of individual materials, period size, volume fraction of insertion, and atomic-level interface quality are the four main parameters to control phonon transport in nanocomposite structures. It is argued that the relative importance of these parameters is system dependent. The equal-layer thickness Si/Ge PSL shows a minimum in the room temperature conductivity for the period size of around 4 nm, and with a moderate amount of interface mass smudging this value lies below the conductivity of SiGe alloy.

Should vitamin D be routinely checked for all chronic obstructive pulmonary disease patients?

AIMS AND OBJECTIVES: This study aimed to compare the vitamin D levels between chronic obstructive pulmonary disease (COPD) patients and healthy controls and to describe the correlation between vitamin D levels and lung functions. METHODS: Fifty COPD patients (cases) and 30 healthy volunteers (controls) were recruited and their serum vitamin D level was measured together with lung function (forced vital capacity and forced expiratory volume in 1 s [FEV1]) by spirometry. vitamin D was categorized as ≤20 nmol/l: deficient, 21-50 nmol/l: inadequate, and ≥51 nmol/l as sufficient. RESULTS: In this case-control cross-sectional study, lower vitamin D levels were associated with lower lung function in both cases as well as controls, the effect being more pronounced in cases. Mean FEV1 at vitamin D ≤20 nmol/l (0.98 ± 0.40 vs. controls 1.93 ± 0.24 with P = 0.006), mean FEV1 at vitamin D 21-50 nmol/l (1.55 ± 0.54 vs. 2.20 ± 0.31 with P = 0.000), and mean FEV1 at vitamin D ≥51 nmol/l (2.06 ± 0.54 vs. 2.20 ± 0.31 with P = 0.002). Moreover, the severity of predicted postbronchodilator FEV1% was also much lower among COPD cohort versus healthy volunteers (mean FEV1%: cases 47.88 ± 14.22 vs. controls 58.76 ± 15.05 with P = 0.002). CONCLUSIONS: Importantly, lung function in both the groups was affected by decreased vitamin D level; decrease in FEV1 was more pronounced among COPD patients compared to controls showing more expiratory airflow limitation. Vitamin D levels are associated with changes in lung function in cases of COPD as well as healthy controls. Larger studies to confirm the association in Indian context are required and routine assessment of vitamin D may be undertaken to obviate the effects of low vitmain D level on lung function.

Rapid detection of drug-resistant Mycobacterium tuberculosis directly from clinical specimens using allele-specific polymerase chain reaction assay.

Background & objectives: Rapid detection of drug resistance in Mycobacterium tuberculosis (MTB) is essential for the efficient control of tuberculosis. Hence, in this study a nested-allele-specific (NAS) PCR, nested multiple allele-specific PCR (NMAS-PCR) and multiple allele-specific (MAS) PCR assays were evaluated that enabled detection of the most common mutations responsible for isoniazid (INH) and rifampicin (RIF) resistance in MTB isolates directly from clinical specimens. Methods: Six pairs of primers, mutated and wild type, were used for the six targets such as codon 516, 526 and 531 of rpoB, codon 315 of katG and C15-T substitution in the promoter region of mabA-inhA using allele-specific (AS) PCR assays (NAS-PCR, NMAS-PCR and MAS-PCR). The performance of AS PCR method was compared with phenotypic drug susceptibility testing (DST). Results: The usefulness of AS PCR assays was evaluated with 391 clinical specimens (251 Acid fast bacilli smear positive and MTB culture positive; 93 smear negative and MTB culture positive; 47 smear positive and MTB culture negative) and 344 MTB culture positive isolates. With culture-based phenotypic DST as a reference standard, the sensitivity and specificity of the NAS-PCR, NMAS-PCR and MAS-PCR assay for drug resistance-related genetic mutation detection were 98.6 and 97.8 per cent for INH, 97.5 and 97.9 per cent for RIF and 98.9 and 100 per cent for multidrug resistance (MDR). Interpretation & conclusions: The performance of AS PCR assays showed that those could be less expensive and technically executable methods for rapid detection of MDR-TB directly from clinical specimens.

No high Tibetan Plateau until the Neogene.

The Late Paleogene surface height and paleoenvironment for the core area of the Qinghai-Tibetan Plateau (QTP) remain critically unresolved. Here, we report the discovery of the youngest well-preserved fossil palm leaves from Tibet. They were recovered from the Late Paleogene (Chattian), ca. 25.5 ± 0.5 million years, paleolake sediments within the Lunpola Basin (32.033°N, 89.767°E), central QTP at a present elevation of 4655 m. The anatomy of palms renders them intrinsically susceptible to freezing, imposing upper bounds on their latitudinal and altitudinal distribution. Combined with model-determined paleoterrestrial lapse rates, this shows that a high plateau cannot have existed in the core of Tibet in the Paleogene. Instead, a deep paleovalley, whose floor was <2.3 km above mean sea level bounded by (>4 km) high mountain systems, formed a topographically highly varied landscape. This finding challenges prevailing views on tectonic processes, monsoon dynamics, and the evolution of Asian biodiversity.

Mode confinement, interface mass-smudging, and sample length effects on phonon transport in thin nanocomposite superlattices.

We employ a semi-ab initio theoretical method to investigate mode confinement, interface mass-smudging, and sample length effects on phonon transport in thin nanocomposite superlattices. We present a detailed comparative study of numerical results showing the reduction in thermal conductivity due to each of these three effects for Si/Ge nanocomposite structures with planar superlattice (SL), embedded nanowire superlattice (NWSL), and embedded nanodot superlattice (NDSL) geometries. Importantly, it is found that any of these three types of thin period systems, with small amounts of interface mass smudging, can exhibit a room-temperature conductivity significantly lower than the SiGe alloy conductivity, providing strong evidence that they could be used as efficient thermoelectric materials. It is also found that the room-temperature conductivity of each of the nanocomposite superlattices shows a weaker sample size dependence than do the component bulk conductivities.

Anharmonic, dimensionality and size effects in phonon transport.

We have developed and employed a numerically efficient semi- ab initio theory, based on density-functional and relaxation-time schemes, to examine anharmonic, dimensionality and size effects in phonon transport in three- and two-dimensional solids of different crystal symmetries. Our method uses third- and fourth-order terms in crystal Hamiltonian expressed in terms of a temperature-dependent Grüneisen's constant. All input to numerical calculations are generated from phonon calculations based on the density-functional perturbation theory. It is found that four-phonon processes make important and measurable contribution to lattice thermal resistivity above the Debye temperature. From our numerical results for bulk Si, bulk Ge, bulk MoS2 and monolayer MoS2 we find that the sample length dependence of phonon conductivity is significantly stronger in low-dimensional solids.

Evaluation of the nutrient profile of Trachyspermum ammi L. seed under the influence of nanoparticles during germination.

Trachyspermum ammi L. commonly known as Ajwain is an annual herb belonging to the family Apiaceae. It is enormously grown in Egypt, Iran, Pakistan, Afghanistan, and India as well as European region. Seeds of Ajwain were highly administered by traditional healers and usually employed for different ailments. Nanomaterials are known to have plant growth promoting effects, which could find applications in agriculture. In this study, the nanoparticles (NPs) showed the potential to enhance the primary metabolites when administered during germination. Therefore, nanoparticles elicitation can be used to increase the productivity, nutritional values and metabolite contents in Trachyspermum ammi L. This study aimed to provide new insight of the potential growth promoting effects of the nanoparticles () on plant system. Different concentrations of two nanoparticles, that is, iron pyrite (FeS2) and molybdenum disulphide (MoS2) at three different concentrations of 25ug/ml, 50ug/ml and 75ug/ml were tested on the seeds of Trachyspermum ammi L. The data indicated that nanoparticles enhanced the seedling growth as greener leafs and increased lengths of epicotyl and hypocotyls were seen. These nanoparticles also showed the potential to increase the contents of primary metabolites during germination and the total soluble protein content in seed was increased in nanoparticles-treated seeds as compared to control. The total protein profiling by SDS-PAGE indicated significant differences in number and molecular weights of protein bands upon exposure to nanoparticles.

Association of Risk Factors and Drug Resistance Pattern in Tuberculosis Patients in North India.

CONTEXT: India is one of the high tuberculosis (TB) burden countries in the world. Improper implementation in the guidelines for the management of TB and high rate of defaults on the part of the patients are most important risk factors for the development of multi-drug resistant TB. AIMS: This study examines the drug resistance profile and the effect of demographic, clinical and behavioral risk factors on the prevalence of TB and multidrug resistance (MDR) in north India. SETTINGS AND DESIGN: This was a prospective, observational study carried out from May 2012 to February 2014 in tertiary care hospital of Varanasi. SUBJECTS AND METHODS: The study was performed on 721 pulmonary and extrapulmonary specimens of suspected TB patients based on history, was subjected for the Ziehl-Neelsen staining and culture on Lowenstein-Jensen (LJ) media. STATISTICAL ANALYSIS: The features of groups were compared by Chi-square (χ2) and odds ratio. RESULTS: Out of 721 clinically suspected pulmonary and extrapulmonary TB patients, 222 (30.8%) patients were smear positive for acid-fast bacilli and 244 (38.3%) were positive for Mycobacterium species cultured on LJ medium. The prevalence of resistance to at least one anti-TB drug was 71.1% and MDR was 53.5%. Age, gender, HIV status, nature of TB, smoking, and alcohol consumption risk factors were significantly associated with TB prevalence; while prior history of TB infection, pervious household exposure, smoking, and alcohol consumption were significantly associated with MDR. CONCLUSION: This study showed a high prevalence of drug resistance TB in this region. It also provides evidence in our circumstance, of the role of prior history of TB infection, alcohol and smoking in increasing the risk of developing TB and MDR-TB. Therefore, it is necessary for the public health community to incorporate and strengthen alcohol and smoking nonparticipation interference in TB control program.

Performance of nested multiplex PCR assay targeting MTP40 and IS6110 gene sequences for the diagnosis of tubercular lymphadenitis.

The conventional methods for diagnosis of tubercular lymphadenitis (TBLN) such as - fine needle aspiration cytology, Ziehl-Neelsen staining and culture have limitations of low sensitivity and/or specificity. So, it becomes essential to develop a rapid, sensitive, and specific method for an early diagnosis of TBLN. Therefore, the present study was conducted to evaluate nested multiplex polymerase chain reaction (nMPCR) targeting MTP40 and IS6110 gene sequences of Mycobacterium tuberculosis and Mycobacterium tuberculosis complex, respectively in 48 successive patients of TBLN and 20 random patients with non-tubercular lymph node lesions. Out of the 48 cases of TBLN, 14 (29.2%) were found to be positive by Ziehl-Neelsen staining, 15 (31.2%) were positive by culture and 43 (89.6%) cases were positive after first round of PCR while 48 (100%) cases were positive by nMPCR assay. The sensitivity and specificity of nMPCR was found to be 100% for the diagnosis of TBLN. The results thus obtained indicate that nMPCR assay is a highly sensitive and specific tool for the diagnosis of TBLN.

Size and dimensionality dependent phonon conductivity in nanocomposites.

We have studied size and dimensionality dependent phonon conductivity of PbTe-PbSe nanocomposites by considering three configurations: superlattice, embedded nanowire and embedded nanodot. Calculations have been performed in the framework of an effective medium theory. The required bulk thermal conductivities of PbTe and PbSe are evaluated by using Callaway's effective relaxation-time theory, and by accounting for relevant scattering mechanism including three-phonon Normal and Umklapp interactions involving acoustic as well as optical branches. The thermal interface resistance is computed using the diffuse mismatch theory. It is found that the size (thickness) and volume fraction of PbSe are the two main factors that control the effective thermal conductivity in these nanocomposites. In particular, for PbSe size d = 10 nm and volume fraction Vf = 0.1, our results predict significant reductions over the weighted average of room-temperature bulk results of 9%, 17% and 15% in the conductivity across the interfaces for the superlattice, embedded nanowire, and nanosphere structures, respectively. For a given Vf, an increase in d reduces the interface density and the effective conductivity varies approximately as [Formula: see text]. It is shown that nanocompositing in any of the three configurations can beat the alloy limit for lattice thermal conductivity.

Differentiation of Mycobacterium tuberculosis complex from non-tubercular mycobacteria by nested multiplex PCR targeting IS6110, MTP40 and 32kD alpha antigen encoding gene fragments.

BACKGROUND: Control of the global burden of tuberculosis is obstructed due to lack of simple, rapid and cost effective diagnostic techniques that can be used in resource poor-settings. To facilitate the early diagnosis of TB directly from clinical specimens, we have standardized and validated the use of nested multiplex PCR, targeting gene fragments IS6110, MTP40 and 32kD α-antigen encoding genes specific for Mycobacterium tuberculosis complex and non-tubercular mycobacteria (NTM), in comparison to smear microscopy, solid culture and single step multiplex PCR. The results were evaluated in comparison to a composite reference standard (CRS) comprising of microbiological results (smear and culture), clinical, radiological and cytopathological findings, clinical treatment and response to anti-tubercular therapy. METHODS: The nested multiplex PCR (nMPCR) assay was evaluated to test its utility in 600 (535 pulmonary and 65 extra-pulmonary specimens) clinically suspected TB cases. All specimens were processed for smear, culture, single step multiplex PCR and nested multiplex PCR testing. RESULTS: Out of 535 screened pulmonary and 65 extra-pulmonary specimens, 329 (61.5%) and 19 (29.2%) cases were culture positive for M. tuberculosis. Based on CRS, 450 patients had "clinical TB" (definitive-TB, probable-TB and possible-TB). Remaining 150 were confirmed "non-TB" cases. For culture, the sensitivity was low, 79.3% for pulmonary and 54.3% for extra-pulmonary cases. The sensitivity and specificity results for nMPCR test were evaluated taken composite reference standard as a gold standard. The sensitivity of the nMPCR assay was 97.1% for pulmonary and 91.4% for extra-pulmonary TB cases with specificity of 100% and 93.3% respectively. CONCLUSION: Nested multiplex PCR using three gene primers is a rapid, reliable and highly sensitive and specific diagnostic technique for the detection and differentiation of M. tuberculosis complex from NTM genome and will be useful in diagnosing paucibacillary samples. Nested multiplex PCR assay was found to be better than single step multiplex PCR for assessing the diagnosis of TB.

Three-phonon scattering processes and thermal conductivity in IV-chalocogenides.

We present a systematic study of allowed three-phonon scattering processes, involving acoustic and optical branches, and their relative roles in explaining the low thermal conductivity κ of IV-chalcogenide thermoelectric materials PbTe, PbSe, PbS, and SnTe. Using numerical results for κ, computed by employing the isotropic continuum scheme, we have examined the extent of the additional contribution the Callaway theory and the Allen theory provide over the single-mode relaxation time theory. Within the Callaway theory, for all these materials the acoustic (TA, LA) and transverse optical (TO) phonons contribute between 10-25% towards κ at and above room temperature, with κ(TO) > κ(TA) > κ(LA). The longitudinal optical (LO) phonons contribute negligibly (<5%) in Pb-chalogenides, but their contribution is larger (22%) than that of TO phonons (18%) in SnTe. Due to the presence of high defect concentration in these materials, the high temperature conductivity varies less strongly than T(-1). In confirmation with experimental measurements, our study finds that below the Debye temperature the resistivity of SnTe varies as the square-root of the point defect concentration.

Cutaneous Cryptococcus: marker for disseminated infection.

Cryptococcosis is an infection caused by the encapsulated yeast, Cryptococcus neoformans, a dimorphic fungus recovered from pigeon excreta, soil, dust and human skin. After a primary infection in the lungs, the disease can disseminate via a haematogenous route to various organs, including the central nervous system and skin, in susceptible individuals. Cryptococcosis can present with a variety of skin and soft tissue manifestations including acneiform lesions, purpura, vesicles, nodules, abscesses, ulcers, granulomas, pustules, draining sinuses and cellulitis. We present a case of a young man with HIV infection who developed molluscum-like cutaneous lesions secondary to pulmonary cryptococcosis. The diagnosis was confirmed by Indian ink preparation of the cutaneous lesions. Primary cutaneous infection occurs rarely due to direct inoculation. Cutaneous lesions are usually secondary and act as a key marker of disseminated infection, especially in patients with impaired cell-mediated immunity, such as those infected with HIV, solid-organ transplant recipients, and those on chronic corticosteroid therapy.

Prediction of recurrence-free survival using a protein expression-based risk classifier for head and neck cancer.

Loco-regional recurrence in 50% of oral squamous cell carcinoma (OSCC) patients poses major challenge for oncologists. Lack of biomarkers that can predict disease aggressiveness and recurrence risk makes the scenario more dismal. On the basis of our earlier global proteomic analyses we identified five differentially expressed proteins in OSCC. This study aimed to develop protein biomarkers-based prognostic risk prediction model for OSCC. Sub-cellular expression of five proteins, S100A7, heterogeneous nuclear ribonucleoproteinK (hnRNPK), prothymosin α (PTMA), 14-3-3ζ and 14-3-3σ was analyzed by immunohistochemistry in test set (282 Indian OSCCs and 209 normal tissues), correlated with clinic-pathological parameters and clinical outcome over 12 years to develop a risk model for prediction of recurrence-free survival. This risk classifier was externally validated in 135 Canadian OSCC and 96 normal tissues. Biomarker signature score based on PTMA, S100A7 and hnRNPK was associated with recurrence free survival of OSCC patients (hazard ratio=1.11; 95% confidence interval 1.08, 1.13, P<0.001, optimism-corrected c-statistic=0.69) independent of clinical parameters. Biomarker signature score stratified OSCC patients into high- and low-risk groups with significant difference for disease recurrence. The high-risk group had median survival 14 months, and 3-year survival rate of 30%, whereas low-risk group survival probability did not reach 50%, and had 3-year survival rate of 71%. As a powerful predictor of 3-year recurrence-free survival in OSCC patients, the newly developed biomarkers panel risk classifier will facilitate patient counseling for personalized treatment.

Tuning phonon properties in thermoelectric materials.

This review article presents a discussion of theoretical progress made over the past several decades towards our understanding of thermoelectric properties of materials. Particular emphasis is placed upon describing recent progress in 'tuning' phonon properties of nanocomposite materials for gaining enhancement of the thermoelectric figure of merit.