Employing neural density functionals to generate potential energy surfaces.

CONTEXT: With the union of machine learning (ML) and quantum chemistry, amid the debate between machine-learned functionals and human-designed functionals in density functional theory (DFT), this paper aims to demonstrate the generation of potential energy surfaces using computations with machine-learned density functional approximation (ML-DFA). A recent research trend is the application of ML in quantum sciences in the design of density functionals such as DeepMind's Deep Learning model (DeepMind21, DM21). Though science reported the state-of-the-art performance of DM21, the opportunity to utilize DeepMind's pretrained DM21 neural networks in computations in quantum chemistry has not yet been tapped. So far in the literature, the Deep Learning density functionals (DM21) have not been applied to generate potential energy surfaces. While the superior accuracy of DM21 has been reported, there is still a scarcity of publications that apply DM21 in calculations in the field. In this context, for the first time in literature, neural density functionals inferring 2D potential energy surfaces (ML-DFA-PES) based on machine-learned DFA-based computational method is contributed in this paper. This paper reports the ML-DFA-generated PES for C4H8, H2O, H2, and H2+ by employing a pretrained DM21m TensorFlow model with cc-pVDZ basis set. In addition, we also analyze the long-range behavior of DM21 based PES to investigate the ability to describe a system at long ranges. Furthermore, we compare PES diagrams from DM21 with popular DFT functionals (b3lyp/ PW6B95) and CCSD(T). METHODS: In this method, 2D potential energy surfaces are obtained using a method that relies upon the neural network's ability to accurately learn the mapping between 3D electron density and exchange-correlation potential. By inserting Deep Learning inference in DFT with a pretrained neural network, self-consistent field (SCF) energy at different geometries along the coordinates of interest is computed, and then, potential energy surfaces are plotted. In this method, first, the electron density is computed mathematically, and this computed 3D electron density is used as a ML feature vector to predict the exchange correlation potential as a ML inference computed by a forward pass of pre-trained DM21 TensorFlow computational graph, followed by the computation of self-consistent field energy at multiple geometries, and then, SCF energies at different bond lengths/angles are plotted as 2D PES. We implement this in a python source code using frameworks such as PySCF and DM21. This paper contributes this implementation in open source. The source code and DM21-DFA-based PES are contributed at https://sites.google.com/view/MLfunctionals-DeepMind-PES .

Living with PTSD amid a global pandemic.

The COVID-19 pandemic has demonstrated itself to be a considerable stressor, especially for those individuals coping with a preexisting mental health disorder. This article contains clinical observations and reflections from two practicing psychologists regarding the impact of the COVID-19 pandemic and associated social conditions on clients with posttraumatic stress disorder. Observations include changes in trauma-related symptom manifestations and therapeutic process issues, particularly in response to social isolation. The authors encourage specific therapeutic considerations and offer suggestions for adapting treatment with regard to these early observations. (PsycInfo Database Record (c) 2020 APA, all rights reserved).

What determines violence among female sex workers in an intimate partner relationship? Findings from North Karnataka, south India.

BACKGROUND: Like other women in India, female sex workers (FSWs) frequently experience violence from their intimate partners (IPs)-a reality that increases their risk of acquiring HIV or other sexually transmitted infections. Less is known about the nature of these intimate relationships or what aspect of the relationship increases the risk of IP violence (IPV). We measured the prevalence and determinants of IPV on FSWs in the context of north Karnataka, India, characterized by high HIV-prevalence and extreme poverty. METHODS: Overall 620 FSWs with an IP participated in a baseline survey conducted for an on-going cluster-randomised controlled trial aiming to evaluate the impact of a multi-level intervention on IPV reduction. We characterize the nature of intimate relationships and explored determinants of severe physical and/or sexual IP violence using univariable and multivariable analyses. RESULTS: The median age of participants was 35 years with 10 years of duration in an intimate relationship. Though most relationships originated from a sex work encounter, 84% stated that IPs did not know they were currently practicing sex work. In past 6 months, the experience of emotional violence was 49% (95%CI:45.2-53.2), physical 33% (95%CI:29.5-37.1) and sexual violence 7% (95%CI:4.8-8.9), while 24% (95%CI:21.0-27.9) FSWs experienced recent severe physical and/or sexual violence from IPs. Factors associated with recent IPV included experience of physical and/or sexual violence from their clients in last 6 months (AOR 2.20; 95%CI: 1.29-3.75), sexual intercourse in the past 1 month when their IP was under the influence of alcohol (AOR 2.30; 95%CI: 1.47-3.59) and providing financial support to their IP (AOR 2.07; 95%CI: 1.28-3.34). CONCLUSIONS: The association between increased risk of violence and provision of financial support to an IP is indicative of gendered power dynamics as men remain dominant irrespective of their financial dependency on FSWs. Interventions are needed that address inequitable gender norms which makes FSWs tolerate violence even though she is not financially dependent on IP. Higher likelihood of violence in presence of alcohol use and FSWs' previous experience of workplace violence linked to IPV call for strengthening the crisis management systems within community-based organisations that can address all forms of violence and associated risk factors. TRIAL REGISTRATION: Clinical Trials NCT02807259.

Tuberculosis among the homeless in Chennai city, South India.

Background: In India from a national perspective, the incidence/prevalence of active tuberculosis (TB) among the homeless are unknown. Methods: Homeless individuals, aged 15 years and above, were screened for TB by radiography and smear examination in Chennai city. Results: 301 individuals were enrolled and screened for TB; 8% (24/301) had chest symptoms; 5.6% (17/301) found X-ray abnormalities. The overall prevalence of TB was 1661/100 000; prevalence of culture-positive TB was 997/100 000 and smear-positive TB was 664/100 000 population. Conclusion: There is a need to address TB control among homeless populations. The current pilot study showed that the prevalence of TB was disproportionately high and there is a need for a larger study with an adequately powered sample size.

Reducing violence and increasing condom use in the intimate partnerships of female sex workers: study protocol for Samvedana Plus, a cluster randomised controlled trial in Karnataka state, south India.

BACKGROUND: Female sex workers (FSWs) are at increased risk of HIV and STIs compared to women in the general population, and frequently experience violence in their working and domestic lives from a variety of perpetrators, which can enhance this risk. While progress has been made in addressing violence by police and clients, little work has been done to understand and prevent violence by intimate partners (IPs) among FSW populations. METHODS: Samvedana Plus is a multi-level intervention programme that works with FSWs, their IPs, the sex worker community, and the general population, and aims to reduce violence and increase consistent condom use within these 'intimate' relationships. The programme involves shifting norms around the acceptability of beating as a form of discipline, challenging gender roles that give men authority over women, and working with men and women to encourage new relationship models based on gender equity and respect. The programme will aim to cover 800 FSWs and their IPs living in 47 villages in Bagalkot district, northern Karnataka. The study is designed to assess two primary outcomes: the proportion of FSWs who report: (i) physical or sexual partner violence; and (ii) consistent condom use in their intimate relationship, within the past 6 months. The evaluation will employ a cluster-randomised controlled trial design, with 50 % of the village clusters (n = 24) randomly selected to receive the intervention for the first 24 months and the remaining 50 % (n = 23) receiving the intervention thereafter. Statisticians will be blinded to treatment arm allocation. The evaluation will use an adjusted, cluster-level intention to treat analysis, comparing outcomes in intervention and control villages at midline (12 months) and endline (24 months). The evaluation design will involve quantitative and qualitative assessments with (i) all FSWs who report an IP (ii) IPs; and process/ implementation monitoring. Baseline data collection was completed in April 2015, and endline data collection is anticipated in May 2017. CONCLUSIONS: This is an innovative intervention programme that aims to address violence by IPs as part of HIV prevention programming with FSWs. Reducing violence is expected to reduce vulnerability to HIV acquisition, and help women to work and live without fear of violence. TRIAL REGISTRATION: Clinical Trials NCT02807259 Jun 24 2016 (retrospectively registered).

Knowledge, Attitude and Practices Regarding HPV Vaccination Among Medical and Para Medical in Students, India a Cross Sectional Study.

BACKGROUND: High risk human papilloma virus (HPV) types 16 and 18 have been proven as central causes of cervical cancer and safety and immunogenicity of HPV vaccines are sufficiently established. Knowledge and practices of HPV vaccination among medical and paramedical students is vital as these may strongly determine intention to recommend vaccination to others in the future. The present study was therefore undertaken to assess the knowledge, attitude and practices regarding cervical cancer screening and HPV vaccination among medical and paramedical students and to analyze factors influencing them. MATERIALS AND METHODS: The present cross sectional study, conducted in a tertiary care teaching hospital in south India, included undergraduate students aged 18 years and above, belonging to medical, dental and nursing streams, after informed written consent. RESULTS: Out of 957 participants, only 430 (44.9%) displayed good knowledge and only 65 (6.8%) had received HPV vaccination. Among the unvaccinated, 433 (48.54%), were not willing to take the vaccine. Concerns regarding the efficacy (30.5%), safety (26.1%) and cost of the vaccine (21.7%) were responsible for this. Age, gender, family history of malignancy and mother's education had no influence on knowledge. Compared to medical students, nursing students had better knowledge (OR-1.49, 95% CI 0.96 to 2.3, p = 0.072) and students of dentistry had poor knowledge (OR-0.50 95% CI 0.36 to 0.70, p <0.001). CONCLUSIONS: The knowledge and uptake of HPV vaccination among medical and paramedical students in India is poor. Targeted health education interventions may have huge positive impact not only on the acceptance of vaccination among them, but also on their intention to recommend the vaccine in future.

Histochemical analysis of polarizing colors of collagen using Picrosirius Red staining in oral submucous fibrosis.

BACKGROUND: Oral Submucous fibrosis (OSMF) is a common potentially malignant disease, which is characterized by generalized fibrosis of the oral soft tissues. It is due to disproportion in the collagen deposition and degradation. The excess deposition of collagen results in juxta epithelial fibro elastic changes and epithelial atrophy. Neoplastic changes in the epithelium usually precede the changes in the connective tissue. The purpose of the study was to evaluate the changes in birefringence of collagen using picrosirius stain and compare with haematoxylin and eosin stained section. MATERIALS & METHODS: The study was conducted on 50 subjects, which included 45 patients diagnosed with different functional and histopathological grades of OSMF and 5 in control group. Picrosirius red stain was used to analyze collagen both histopathologically and qualitatively using polarizing microscopy. Chi-square test at p value <0.05 was used to analyze the results and the significance was tabulated. RESULTS: Collagen fibers showed mixed birefringence with a shift in polarizing colour from yellow to red-orange in lamina propria, around the muscle and blood vessels, which was correlating with the conventional H&E stain. CONCLUSION: The results of present study show a significant change in birefringence of collagen between the various components of connective tissue. This change in birefringence colors and arrangement of collagen fibers might give an assumption of impending neoplastic change in OSMF. How to cite the article: Velidandla S, Gaikwad P, Ealla KK, Bhorgonde KD, Hunsingi P, Kumar A. Histochemical analysis of polarizing colors of collagen using Picrosirius Red staining in oral submucous fibrosis. J Int Oral Health 2014;6(1):33-8.

Inhibition of enteropathogenic Escherichia coli adhesion on host epithelial cells by Holarrhena antidysenterica (L.) WALL.

Bacterial adhesion is the first step in the sequence of events leading to infection. Previous data are available on the effect of Holarrhena antidysenterica on antidiarrhoeal and antibacterial action, but there is little information on the mechanism of action of the various aspects of EPEC-induced diarrhoea, namely adherence and translocation of the effector molecule to intestinal epithelial cells. The aim of the present study was to investigate the effects of alkaloids of Holarrhena antidysenterica (AHA) on interference in the mechanism of enteropathogenic Escherichia coli (EPEC) adhesion on host epithelial cells (INT 407 and HEp2). To determine the impact of AHA on epithelial cells, cytotoxicity (LDH), adherence, apoptotic and ultrastructural studies were performed. To analyse the effect of AHA on EPEC secreted proteins, especially EspD, INT 407 monolayers were infected with EPEC and AHA-treated EPEC, followed by immunoblotting, probed with anti EspD antisera. The maximum percentage of LDH leakage was reduced in AHA-treated EPEC (400 microg/mL) in both cell lines. Reduced bacterial adherence was observed under light microscopy and altered apoptotic changes were visualized using propidium iodide staining in conjunction with fluorescence microscopy, in both cell lines infected with AHA-treated EPEC and these results were confirmed with transmission electron microscope images. The suppression of type III secretory proteins (TTSPs), EspD ( approximately 40 kDa), was detected in INT 407 cells infected with AHA-treated EPEC. In conclusion, AHA reduces initial bacterial adhesion to intact epithelial cells and it may exert an antiadherence effect against the pathogenesis of EPEC in host epithelial cells. Thus, the investigations provide a rational basis for the treatment of EPEC-mediated diarrhoea with AHA.

Highly sensitive measurements of PNA-DNA hybridization using oxide-etched silicon nanowire biosensors.

The highly sensitive and sequence-specific detection of single-stranded oligonucleotides using nonoxidized silicon nanowires (SiNWs) is demonstrated. To maximize device sensitivity, the surface of the SiNWs was functionalized with a densely packed organic monolayer via hydrosilylation, subsequently immobilized with peptide nucleic acid (PNA) capable of recognizing the label-free complementary target DNA. Because of the selective functionalization of the SiNWs, binding competition between the nanowire and the underlying oxide is avoided. Transmission electron microscopy was conducted to clearly differentiate the SiNW surface before and after removal of SiO(2). Fluorescence microscopy was used to further realize the selectivity of the oxide-etched chemistry on the SiNWs and sequence specificity of PNA-DNA hybridization. The concentration-dependent resistance change measurements upon hybridization of PNA-DNA show that detection limit down to 10fM can be obtained. The SiNW devices also reveal the capability of an obvious discrimination against mismatched sequences. Among several efforts being made to improve detection sensitivity, this work addresses one significant issue regarding surface functionalization which enables highly sensitive biomolecular sensing with SiNWs.

DNA sensing by silicon nanowire: charge layer distance dependence.

To provide a comprehensive understanding of the field effect in silicon nanowire (SiNW) sensors, we take a systematic approach to fine tune the distance of a charge layer by controlling the hybridization sites of DNA to the SiNW preimmobilized with peptide nucleic acid (PNA) capture probes. Six target DNAs of the same length, but differentiated successively by three bases in the complementary segment, are hybridized to the PNA. Fluorescent images show that the hybridization occurs exclusively on the SiNW surface between the target DNAs and the PNA. However, the field-effect response of the SiNW sensor decreases as the DNA (charge layer) moves away from the SiNW surface. Theoretical analysis shows that the field effect of the SiNW sensor relies primarily on the location of the charge layer. A maximum of 102% change in resistance is estimated based on the shortest distance of the DNA charge layer (4.7 A) to the SiNW surface.

Organic micro-pollutant removal in liquid-phase using carbonized silk cotton hull.

Phenolic compounds constitute one of the major pollutants in the modern world. Although many physical and chemical treatment technologies for their removal exist, most of them are economically not feasible. The present study was aimed at using silk cotton hull, a potent agricultural waste as an adsobent for removal of 2,4-dichlorophenol (2,4-DCP), which was used as a model phenolic compound. The process parameters were investigated and optimized conditions were determined. The equilibrium time was found to be 60 and 80 min for 10 and 20 mg/L and 100 min for 30 and 40 mg/L 2,4-DCP concentrations, respectively. Among the kinetic models applied, pseudo-second order model fitted well. The maximum adsorption capacity was 16.0 mg/g by Langmuir isotherm. Acidic pH was found favorable for the adsorption of 2,4-DCP. Studies on pH effect and desorption seemed to show that chemisorption played a major role in the adsorption process. In thermodynamic study, the change in entropy (DeltaS0) and heat of adsorption (DeltaH0) of silk cotton hull carbon (SCHC) was estimated as 14.01 J/(mol x K) and 3.04 kJ/mol, respectively. SCHC as adsorbent for removal of 2,4-DCP from aqueous solution, is effective, inexpensive, indigenous, reusable, has low treatment time and is easily available in large quantities as waste there by significantly lowers the cost of wastewater treatment.

Silicon nanowire arrays for label-free detection of DNA.

Arrays of highly ordered n-type silicon nanowires (SiNW) are fabricated using complementary metal-oxide semiconductor (CMOS) compatible technology, and their applications in biosensors are investigated. Peptide nucleic acid (PNA) capture probe-functionalized SiNW arrays show a concentration-dependent resistance change upon hybridization to complementary target DNA that is linear over a large dynamic range with a detection limit of 10 fM. As with other SiNW biosensing devices, the sensing mechanism can be understood in terms of the change in charge density at the SiNW surface after hybridization, the so-called "field effect". The SiNW array biosensor discriminates satisfactorily against mismatched target DNA. It is also able to monitor directly the DNA hybridization event in situ and in real time. The SiNW array biosensor described here is ultrasensitive, non-radioactive, and more importantly, label-free, and is of particular importance to the development of gene expression profiling tools and point-of-care applications.

Kinetic and isothermal studies on liquid-phase adsorption of 2,4-dichlorophenol by palm pith carbon.

Adsorption studies were conducted to study the removal of 2,4-dichlorophenol (2,4-DCP) from aqueous solution on palm pith carbon under varying experimental conditions such as agitation time, adsorbent dose, pH and temperature. Higher 2,4-DCP was removed with decrease in the initial concentration of 2,4-DCP and increase in amount of adsorbent used. Kinetic study showed that the adsorption of 2,4-DCP on palm pith carbon was a gradual process. Adsorption capacities were 19.16 mg/g for the particle size of 250-500 microm. The equilibrium time was 60 and 80 min for 10 and 20 mg/L and 100 min for both 30 and 40 mg/L phenol concentrations, respectively. Acidic pH was favourable for the adsorption of 2,4-DCP. Studies on pH effect and desorption showed that chemisorption seemed to play a major role in the adsorption process. Thermodynamic study showed that adsorption of 2,4-DCP on palm pith carbon was more favoured. The change in entropy (DeltaS0) and heat of adsorption (DeltaH0) of palm pith carbon was estimated as 30.72 J/mol/k and 7.16 kJ/mol, respectively. The high positive value of change in Gibbs free energy indicated the feasible and spontaneous adsorption of 2,4-DCP on palm pith carbon. The results indicated that palm pith carbon was an attractive candidate for removing phenols from wastewater.

Experimental and kinetic studies on methylene blue adsorption by coir pith carbon.

Varying the parameters such as agitation time, dye concentration, adsorbent dose, pH and temperature carried out the potential feasibility of thermally activated coir pith carbon prepared from coconut husk for removal of methylene blue. Greater percentage of dye was removed with decrease in the initial concentration of dye and increase in amount of adsorbent used. Kinetic study showed that the adsorption of dye on coir pith carbon was a gradual process. Lagergren first-order, second-order, intra particle diffusion model and Bangham were used to fit the experimental data. Equilibrium isotherms were analysed by Langmuir, Freundlich, Dubnin-Radushkevich, and Tempkin isotherm. The adsorption capacity was found to be 5.87 mg/g by Langmuir isotherm for the particle size 250-500 microm. The equilibrium time was found to be 30 and 60 min for 10 and 20 mg/L and 100 min for 30, 40 mg/L dye concentrations, respectively. A maximum removal of 97% was obtained at natural pH 6.9 for an adsorbent dose of 100 mg/50 mL and 100% removal was obtained for an adsorbent dose of 600 mg/50 mL of 10 mg/L dye concentration. The pH effect and desorption studies suggest that chemisorption might be the major mode of the adsorption process. The change in entropy (DeltaS0) and heat of adsorption (DeltaH0) of coir pith carbon was estimated as 117.20 J/mol/K and 30.88 kJ/mol, respectively. The high negative value of change in Gibbs free energy indicates the feasible and spontaneous adsorption of methylene blue on coir pith carbon.

Childhood polyarteritis nodosa: a clinical diagnosis.

A six-year old boy presented with dry gangrene of toes and fingers with hypertension with no other systemic abnormalities. He had persistently high inflammatory parameters, was diagnosed as childhood classic polyarteritis nodosa and showed improvement with immunosuppressants along with antihypertensives. Toe gangrene required amputation in view of superadded infection.

The pharyngeal-cervical-brachial form of Guillain-Barré syndrome in childhood.

Variant forms of the Guillain-Barré syndrome are characterized by their localized or regional involvement of the peripheral and autonomic nerves. As there is no single clinical or serologic marker for Guillain-Barré syndrome, diagnosis of this condition is based upon consistent clinical, laboratory, and neurophysiologic findings, with exclusion of other conditions mimicking this disorder. Recognition of atypical cases enables anticipatory monitoring for disease complications and identifies therapeutic options for affected children. A regional variant with predominant facial, neck, and arm weakness without sensory loss has been reported in adults but only rarely described in childhood. This study reports clinical and neurophysiologic findings in two children with the pharyngeal-cervical-brachial form of Guillain-Barré syndrome. These are the youngest cases of this uncommon disorder reported to date.

Antibacterial and antidiarrhoeal effects of alkaloids of Holarrhena antidysenterica WALL.

The alkaloids from the ethanolic extract of H. antidysenterica seeds were evaluated for their antibacterial activity against clinical isolates of enteropathogenic Escherichia coli (EPEC) in vitro, and their antidiarrhoeal activity on castor oil-induced diarrhoea in rats, in vivo. The plasmid DNA, whole cell lysate and outer membrane protein profile of a clinical isolate of EPEC was determined in presence of alkaloids of H. antidysenterica. The disc diffusion and agar well diffusion methods were used to evaluate the antibacterial efficacy. The alkaloids showed strong antibacterial activity against EPEC strains. In castor oil-induced diarrhoea, alkaloids reduced the diarrhoea with decrease in the number of wet faeces in pretreated rats at a dose of 200-800 mg/kg. The loss of plasmid DNA and suppression of high molecular weight proteins were observed on alkaloids treatment. Taking into account the multiple antibiotic resistance of EPEC, the results suggest usefulness of alkaloids of H. antidysenterica seeds as antibacterial and antidiarrhoeal agents.

Removal of phenol and chlorophenols from water by coir pith carbon: equilibrium and rate studies.

Batch mode studies were conducted to study the removal of phenol, 2,4,6-Trichlorophenol (TCP) and Pentachlorophenol (PCP) from aqueous solution on coir pith carbon by adsorption process under varying experimental conditions such as agitation time, adsorbent dose, pH and temperature. Kinetics of adsorption obeyed second order rate equation and the rate constant was found to be in the range 0.0098-0.0672, 0.0949-0.8801 and 0.172-0.305 g/mg/min for phenol, TCP and PCP respectively. Equilibrium adsorption data follow Langmuir isotherm for phenol and PCP and the adsorption capacities were found to be 48.3 mg and 3.7 mg/g, respectively. For TCP, adsorption followed Freundlich isotherm only. Acidic pH was favorable for the adsorption of all the chlorophenols. Studies on pH effect and desorption show that chemisorption seems to play a major rule in the adsorption process. The positive values of H0 24.99, 18.69, and 8.907 kJ/mol for phenol, TCP and PCP respectively, confirm the endothermic nature of adsorption.

Adsorptive removal of 2-chlorophenol by low-cost coir pith carbon.

Adsorption of 2-chlorophenol (2-CP) by coir pith carbon was carried out by varying the parameters such as agitation time, 2-CP concentration, adsorbent dose, pH and temperature. Adsorption equilibrium reached at 40, 60, 80 and 100 min for 2-CP concentration of 10, 20, 30 and 40 mg/l, respectively. Adsorption followed second-order kinetics. The adsorption equilibrium data obeyed Freundlich isotherm. Acidic pH was favorable for the adsorption of 2-CP. Desorption studies showed that chemisorption plays a major role in the adsorption process.