Color accuracy and reproducibility in whole slide imaging scanners.

We propose a workflow for color reproduction in whole slide imaging (WSI) scanners, such that the colors in the scanned images match to the actual slide color and the inter-scanner variation is minimum. We describe a new method of preparation and verification of the color phantom slide, consisting of a standard IT8-target transmissive film, which is used in color calibrating and profiling the WSI scanner. We explore several International Color Consortium (ICC) compliant techniques in color calibration/profiling and rendering intents for translating the scanner specific colors to the standard display (sRGB) color space.

Alternate wetting and drying irrigation maintained rice yields despite half the irrigation volume, but is currently unlikely to be adopted by smallholder lowland rice farmers in Nepal.

Alternate wetting and drying (AWD) irrigation can save water while maintaining rice yields, but in some countries its adoption by farmers remains limited. Key knowledge gaps include the effect of AWD on early vegetative vigor and its relationship with yield; the effects of AWD on yield and water use efficiency of local cultivars used by smallholder farmers; and the socio-economic factors influencing current irrigation scheduling. To address these questions, an on-farm field trial of dry-season () rice, comparing two locally important cultivars (Hardinath-1 and CH-45) under AWD imposed from 1 week after transplanting to flowering and continuous flooding (CF), was carried out in Agyauli in the central Terai region of Nepal, and triangulated with social research methods exploring the rationale for current irrigation scheduling and perceptions of AWD.

GeneXpert MTB/RIF assay as initial test for diagnosis of tuberculous meningitis.

Tuberculous meningitis (TBM) remains the most dangerous form of tuberculosis with high mortality and potential complications. The prompt diagnosis and treatment of this condition remains a key for better prognosis. A 39-year-old woman presented with severe headache, fever, nausea and vomiting, with a history of headache for a month.

Camphor: an herbal medicine causing grand mal seizures.

Camphor is usually used in the USA to repel insects, but it is widely used in other countries as an herb. We report the case of a 52-year-old previously healthy Nepali man who ingested approximately 10 g of pure camphor with therapeutic intention. He developed grand mal seizures, and was evaluated in an emergency room.

The use of human cornea organotypic cultures to study herpes simplex virus type 1 (HSV-1)-induced inflammation.

Purpose: To determine the utility of human organotypic cornea cultures as a model to study herpes simplex virus type 1 (HSV-1)-induced inflammation and neovascularization.

Methods: Human organotypic cornea cultures were established from corneas with an intact limbus that were retrieved from donated whole globes. One cornea culture was infected with HSV-1 (10(4) plaque-forming units), while the other cornea from the same donor was mock-infected.

The Application of GeneXpert MTB/RIF for Smear-Negative TB Diagnosis as a Fee-Paying Service at a South Asian General Hospital.

The GeneXpert MTB/RIF assay (Xpert) is a novel automated diagnostic tool for tuberculosis but its optimal placement in the healthcare system has not been determined. The objective of this study was to determine the possibility of additional case detection for pulmonary tuberculosis (PTB) by offering Xpert to smear-negative patients in a low-HIV burden setting with no Mycobacterium tuberculosis (M.tb.

Typhoid vaccine introduction: An evidence-based pilot implementation project in Nepal and Pakistan.

The World Health Organization (WHO) in 2008 recommended the use of currently licensed typhoid vaccines using a high risk or targeted approach. The epidemiology of disease and the vaccine characteristics make school-based vaccination most feasible in reducing typhoid disease burden in many settings. To assess feasibility of school-based typhoid vaccination, two districts in Kathmandu, Nepal and two towns in Karachi, Pakistan were selected for pilot program.

Hindbrain lactate regulates preoptic gonadotropin-releasing hormone (GnRH) neuron GnRH-I protein but not AMPK responses to hypoglycemia in the steroid-primed ovariectomized female rat.

Steroid positive-feedback activation of the gonadotropin-releasing hormone (GnRH)-pituitary luteinizing hormone (LH) neuroendocrine axis propagates the pre ovulatory LH surge, a crucial component of female reproduction. Our work shows that this key event is restrained by inhibitory metabolic input from hindbrain A2 noradrenergic neurons. GnRH neurons express the ultra-sensitive energy sensor adenosine 5'-monophosphate-activated protein kinase (AMPK); here, we investigated the hypothesis that GnRH nerve cell AMPK and peptide neurotransmitter responses to insulin-induced hypoglycemia are controlled by hindbrain lack of the oxidizable glycolytic end-product L-lactate.

Profile of skin biopsies and patterns of skin cancer in a tertiary care center of Western Nepal.

Background: Skin biopsy is the method to assist clinicians to make definite dermatological diagnosis which further helps in holistic management. Skin cancers are relatively rare clinical diagnosis in developing countries like Nepal, but the prevalence is on rise.

Objectives: To investigate the profile of skin biopsies and frequencies and pattern of skin cancers in a tertiary care centre of Western Nepal.

Mechanochemical Sensing: A Biomimetic Sensing Strategy.

Existing biosensors employ two major components: analyte recognition and signal transduction. Although specificity is achieved through analyte recognition, sensitivity is usually enhanced through a chemical amplification stage that couples the two main units in a sensor. Although highly sensitive, the extra chemical amplification stage complicates the sensing protocol.

Electron spin resonance scanning probe spectroscopy for ultrasensitive biochemical studies.

Electron spin resonance (ESR) spectroscopy's affinity for detecting paramagnetic free radicals, or spins, has been increasingly employed to examine a large variety of biochemical interactions. Such paramagnetic species are broadly found in nature and can be intrinsic (defects in solid-state materials systems, electron/hole pairs, stable radicals in proteins) or, more often, purposefully introduced into the material of interest (doping/attachment of paramagnetic spin labels to biomolecules of interest). Using ESR to trace the reactionary path of paramagnetic spins or spin-active proxy molecules provides detailed information about the reaction's transient species and the label's local environment.

Therapist competence in global mental health: Development of the ENhancing Assessment of Common Therapeutic factors (ENACT) rating scale.

Lack of reliable and valid measures of therapist competence is a barrier to dissemination and implementation of psychological treatments in global mental health. We developed the ENhancing Assessment of Common Therapeutic factors (ENACT) rating scale for training and supervision across settings varied by culture and access to mental health resources. We employed a four-step process in Nepal: (1) Item generation: We extracted 1081 items (grouped into 104 domains) from 56 existing tools; role-plays with Nepali therapists generated 11 additional domains.

Low dietary diversity and micronutrient adequacy among lactating women in a peri-urban area of Nepal.

Objective: The main objectives were to assess the adequacy of the micronutrient intakes of lactating women in a peri-urban area in Nepal and to describe the relationships between micronutrient intake adequacy, dietary diversity and sociodemographic variables.

Design: A cross-sectional survey was performed during 2008-2009. We used 24 h dietary recall to assess dietary intake on three non-consecutive days and calculated the probability of adequacy (PA) of the usual intake of eleven micronutrients and the overall mean probability of adequacy (MPA).

Predictors of duration and treatment failure of severe pneumonia in hospitalized young Nepalese children.

Background: Pneumonia in young children is still the most frequent cause of death in developing countries. We aimed to identify predictors for recovery and treatment failure in children hospitalized with severe pneumonia.

Methods: We enrolled 610 Nepalese children, aged 2 - 35 months from February 2006 to June 2008.

Fungi isolated from Miscanthus and sugarcane: biomass conversion, fungal enzymes, and hydrolysis of plant cell wall polymers.

Background: Biofuel use is one of many means of addressing global change caused by anthropogenic release of fossil fuel carbon dioxide into Earth's atmosphere. To make a meaningful reduction in fossil fuel use, bioethanol must be produced from the entire plant rather than only its starch or sugars. Enzymes produced by fungi constitute a significant percentage of the cost of bioethanol production from non-starch (i.

Pharmacy workers in Nepal can provide the correct information about using mifepristone and misoprostol to women seeking medication to induce abortion.

In Nepal, despite policy restrictions, both registered and unregistered brands of mifepristone and misoprostol can easily be obtained at pharmacies. Since many women visit pharmacies for abortion information, ensuring that they receive effective care from pharmacy workers remains an important challenge. We conducted an operations research study to examine whether trained pharmacy workers can correctly provide information on safe use of mifepristone and misoprostol for early first trimester medical abortion.

The role of auxiliary nurse-midwives and community health volunteers in expanding access to medical abortion in rural Nepal.

Medical abortion was introduced in Nepal in 2009, but rural women's access to medical abortion services remained limited. We conducted a district-level operations research study to assess the effectiveness of training 13 auxiliary nurse-midwives as medical abortion providers, and 120 female community health volunteers as communicators and referral agents for expanding access to medical abortion for rural women. Interviews with service providers and women who received medical abortion were undertaken and service statistics were analysed.

Dorsomedial hindbrain catecholamine regulation of hypothalamic astrocyte glycogen metabolic enzyme protein expression: Impact of estradiol.

The brain astrocyte glycogen reservoir is a vital energy reserve and, in the cerebral cortex, subject among other factors to noradrenergic control. The ovarian steroid estradiol potently stimulates nerve cell aerobic respiration, but its role in glial glycogen metabolism during energy homeostasis or mismatched substrate supply/demand is unclear. This study examined the premise that estradiol regulates hypothalamic astrocyte glycogen metabolic enzyme protein expression during normo- and hypoglycemia in vivo through dorsomedial hindbrain catecholamine (CA)-dependent mechanisms.

Ocular manifestations of childhood acute leukemia in a tertiiary level eye centre of Kathmandu, Nepal.

Introduction: In some instances, the understanding of the ocular manifestations in childhood leukemia is not only important to establish the diagnosis but also reflects the disease state and prognosis.

Objective: To study the ocular manifestations of childhood acute leukemia among the children attending a tertiary-level hospital in Nepal.

Materials And Methods: A cross-sectional, descriptive study was undertaken at the B.

An anthropometric study to evaluate the correlation between the occlusal vertical dimension and length of the thumb.

Background: Establishment of proper occlusal vertical dimension (OVD) is one of the important tasks for successful prosthodontic therapy. An ideal method for determining OVD in terms of cost, time, and instrument requirements has been sought in prosthodontics by various investigators. However, no such single method has been formulated.

Craniometric analysis for estimation of stature in Nepalese population--A study on an autopsy sample.

Establishing the identity of the deceased becomes essential when highly decomposed bodies, mutilated body parts or skeletal remains are recovered from mass fatality sites. In these situations, estimation of stature along with other parameters such as age, sex and race/ethnicity becomes important to establish the biological profile of the deceased. Following the Maoist insurgency in Nepal, there have been numerous discoveries of unidentified human remains in mass graves or otherwise.

Use of nucleoside analogs in patients with chronic hepatitis B in Nepal: A prospective cohort study in a single hospital.

Aim: There still remain many concerns about the present status of antiviral therapy for chronic hepatitis B in developing countries in Asia, where the monitoring systems of virological markers have not been well established, despite the high prevalence of hepatitis B virus (HBV) infection. To investigate it in Nepal, this prospective cohort study was conducted at the Teaching Hospital of Tribhuvan University in Kathmandu.

Methods: From 2007 to 2012, 65 patients were consecutively enrolled, 44 of whom received nucleoside analogs (NA), such as lamivudine (LMV), adefovir or tenofovir (TDF), on the decision of the local hepatologist.

Correlation between microbial community and granule conductivity in anaerobic bioreactors for brewery wastewater treatment.

Prior investigation of an upflow anaerobic sludge blanket (UASB) reactor treating brewery wastes suggested that direct interspecies electron transfer (DIET) significantly contributed to interspecies electron transfer to methanogens. To investigate DIET in granules further, the electrical conductivity and bacterial community composition of granules in fourteen samples from four different UASB reactors treating brewery wastes were investigated. All of the UASB granules were electrically conductive whereas control granules from ANAMMOX (ANaerobic AMMonium OXidation) reactors and microbial granules from an aerobic bioreactor designed for phosphate removal were not.

Interaction of G-quadruplexes in the full-length 3' human telomeric overhang.

The 3' human telomeric overhang provides ample opportunities for the formation and interaction of G-quadruplexes, which have shown impacts on many biological functions including telomerase activities in the telomere region. However, in the few investigations on DNA constructs that approach to the full length of the human telomeric overhang, the presence of higher-order quadruplex-quadruplex interactions is still a subject of debate. Herein, we employed dynamic splint ligation (DSL) to prepare a DNA construct, 5'-(TTAGGG)24 or 24G, which has the length comparable to the full stretch of 3' human telomeric overhang.