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Information on species distribution range is a prerequisite for setting conservation strategies. Conservation efforts in Nepal have been focused on flagship species, such as Bengal Tiger (Panthera tigris), Asian Elephant (Elephas maximus) and Greater One-horned Rhinoceros (Rhinoceros unicornis). By contrast, distribution data and conservation efforts for other mammalian species are scarce. Here we documented the spatial locations of 27 mammal species based on direct sightings and photographic evidence from 70 m to 4,800 m of elevation across Nepal. We mapped their geographic distributions, delineated their elevation ranges and summarized the potential threats within their distribution ranges. We observed expanded elevation range for c. 30% of the 27 species (8 species), with the most noticeable upward expansion of the Common Palm Civet (Paradoxurus hermaphroditus) from <1,500 m to 2,990 m, and downward expansion of the Fawn-colored Mouse (Mus cervicolor) from >1,150 m to 200 m. These updated, high-quality spatial information on a subset of Nepal’s diverse mammalian fauna, highlight new opportunities to study the effects of climate change on mammals in the Himalayan region. [ABSTRACT FROM AUTHOR]

Purpose: To evaluate the efficacy of training programmes for the village health practitioners aimed at improving primary orthopaedic and trauma care in our rural setting. Materials & Methods: Six year prospective study of training workshops in local health institutions was carried out using locally available manpower and materials. Results: After 6 years the evaluation of this programme shows a significantly improved (p < 0.05) knowledge base and working skills after completion of training workshop. Summary: To avoid unnecessary complications, effective primary health care provided by an appropiately trained person should be available at the peripheral level. This training programme seems successful in achieving this goal and hence needs adoption for wider use in Nepal. [ABSTRACT FROM AUTHOR]

Significance: Lensless digital inline holographic microscopy (LDIHM) is an emerging quantitative phase imaging modality that uses advanced computational methods for phase retrieval from the interference pattern. The existing end-to-end deep networks require a large training dataset with sufficient diversity to achieve high-fidelity hologram reconstruction. To mitigate this data requirement problem, physics-aware deep networks integrate the physics of holography in the loss function to reconstruct complex objects without needing prior training. However, the data fidelity term measures the data consistency with a single low-resolution hologram without any external regularization, which results in a low performance on complex biological data., Aim: We aim to mitigate the challenges with trained and physics-aware untrained deep networks separately and combine the benefits of both methods for high-resolution phase recovery from a single low-resolution hologram in LDIHM., Approach: We propose a hybrid deep framework (HDPhysNet) using a plug-and-play method that blends the benefits of trained and untrained deep models for phase recovery in LDIHM. The high-resolution phase is generated by a pre-trained high-definition generative adversarial network (HDGAN) from a single low-resolution hologram. The generated phase is then plugged into the loss function of a physics-aware untrained deep network to regulate the complex object reconstruction process., Results: Simulation results show that the SSIM of the proposed method is increased by 0.07 over the trained and 0.04 over the untrained deep networks. The average phase-SNR is elevated by 8.2 dB over trained deep models and 9.8 dB over untrained deep networks on the experimental biological cells (cervical cells and red blood cells)., Conclusions: We showed improved performance of the HDPhysNet against the unknown perturbation in the imaging parameters such as the propagation distance, the wavelength of the illuminating source, and the imaging sample compared with the trained network (HDGAN). LDIHM, combined with HDPhysNet, is a portable and technology-driven microscopy best suited for point-of-care cytology applications., (© 2024 The Authors.)

Significance: Artificial intelligence (AI) has become a prominent technology in computational imaging over the past decade. The expeditious and label-free characteristics of quantitative phase imaging (QPI) render it a promising contender for AI investigation. Though interferometric methodologies exhibit potential efficacy, their implementation involves complex experimental platforms and computationally intensive reconstruction procedures. Hence, non-interferometric methods, such as transport of intensity equation (TIE), are preferred over interferometric methods., Aim: TIE method, despite its effectiveness, is tedious as it requires the acquisition of many images at varying defocus planes. The proposed methodology holds the ability to generate a phase image utilizing a single intensity image using generative adversarial networks (GANs). We present a method called TIE-GANs to overcome the multi-shot scheme of conventional TIE., Approach: The present investigation employs the TIE as a QPI methodology, which necessitates reduced experimental and computational efforts. TIE is being used for the dataset preparation as well. The proposed method captures images from different defocus planes for training. Our approach uses an image-to-image translation technique to produce phase maps and is based on GANs. The main contribution of this work is the introduction of GANs with TIE (TIE:GANs) that can give better phase reconstruction results with shorter computation times. This is the first time the GANs is proposed for TIE phase retrieval., Results: The characterization of the system was carried out with microbeads of 4    μ m size and structural similarity index (SSIM) for microbeads was found to be 0.98. We demonstrated the application of the proposed method with oral cells, which yielded a maximum SSIM value of 0.95. The key characteristics include mean squared error and peak-signal-to-noise ratio values of 140 and 26.42 dB for oral cells and 100 and 28.10 dB for microbeads., Conclusions: The proposed methodology holds the ability to generate a phase image utilizing a single intensity image. Our method is feasible for digital cytology because of its reported high value of SSIM. Our approach can handle defocused images in such a way that it can take intensity image from any defocus plane within the provided range and able to generate phase map., (© 2024 The Authors.)

Global eradication of poliovirus remains elusive, and it is critical to develop next generation vaccines and antivirals. In support of this goal, we map the epitope of human monoclonal antibody 9H2 which is able to neutralize the three serotypes of poliovirus. Using cryo-EM we solve the near-atomic structures of 9H2 fragments (Fab) bound to capsids of poliovirus serotypes 1, 2, and 3. The Fab-virus complexes show that Fab interacts with the same binding mode for each serotype and at the same angle of interaction relative to the capsid surface. For each of the Fab-virus complexes, we find that the binding site overlaps with the poliovirus receptor (PVR) binding site and maps across and into a depression in the capsid called the canyon. No conformational changes to the capsid are induced by Fab binding for any complex. Competition binding experiments between 9H2 and PVR reveal that 9H2 impedes receptor binding. Thus, 9H2 outcompetes the receptor to neutralize poliovirus. The ability to neutralize all three serotypes, coupled with the critical importance of the conserved receptor binding site make 9H2 an attractive antiviral candidate for future development., (© 2023. Springer Nature Limited.)

White-nose syndrome (WNS), responsible for the mass mortality of North American bats, lacks economically viable and practical in vitro models for Pseudogymnoascus destructans infection, the causative agent of WNS. Not only are many susceptible North American insectivorous bats nearing extinction and, thus, scarce for experimental studies, but they are difficult to care for and maintain in captivity because of their specialized habitats and diets. In this study, we explored porcine ears as a potential substrate for studying infection development and the dynamics of P. destructans growth in the laboratory. Porcine ear skin shares many tissue-level similarities with bat skin and is a readily available resource. We found the porcine ear model provided a substrate faithfully mimicking external P. destructans colony morphology and internal histology similar to what is seen with P. destructans infections in bat wing membranes. This model provided a major advance by distinguishing virulence attributes between a wild-type Pseudogymnoascus destructans strain harboring a partitivirus common to all North American strains of the fungus and an isogenic virus-cured P. destructans strain. ImageJ analysis showed that the cured P. destructans strain was reduced significantly in ability to produce hyphal cover and showed less spore production on porcine skin. Taken together, these results strengthen our previous finding that the partitivirus infection has a role in WNS and provides a valuable model host tool in understanding P. destructans virulence factors for therapeutic application. IMPORTANCE This work describes an important insight into the role of Pseudogymnoascus destructans partitivirus in fungal biology and provides a model system for studying white-nose syndrome in bats, which has decimated North American populations.

Understanding the dynamics of white-nose syndrome spread in time and space is an important component for the disease epidemiology and control. We reported earlier that a novel partitivirus, Pseudogymnoascus destructans partitivirus-pa, had infected the North American isolates of Pseudogymnoascus destructans, the fungal pathogen that causes white-nose syndrome in bats. We showed that the diversity of the viral coat protein sequences is correlated to their geographical origin. Here we hypothesize that the geographical adaptation of the virus could be used as a proxy to characterize the spread of white-nose syndrome. We used over 100 virus isolates from diverse locations in North America and applied the phylogeographic analysis tool BEAST to characterize the spread of the disease. The strict clock phylogeographic analysis under the coalescent model in BEAST showed a patchy spread pattern of white-nose syndrome driven from a few source locations including Connecticut, New York, West Virginia, and Kentucky. The source states had significant support in the maximum clade credibility tree and Bayesian stochastic search variable selection analysis. Although the geographic origin of the virus is not definite, it is likely the virus infected the fungus prior to the spread of white-nose syndrome in North America. We also inferred from the BEAST analysis that the recent long-distance spread of the fungus to Washington had its root in Kentucky, likely from the Mammoth cave area and most probably mediated by a human. The time to the most recent common ancestor of the virus is estimated somewhere between the late 1990s to early 2000s. We found the mean substitution rate of 2 X 10-3 substitutions per site per year for the virus which is higher than expected given the persistent lifestyle of the virus, and the stamping-machine mode of replication. Our approach of using the virus as a proxy to understand the spread of white-nose syndrome could be an important tool for the study and management of other infectious diseases., Competing Interests: The authors have declared that no competing interests exist.

White-nose syndrome is one of the most lethal wildlife diseases, killing over 5 million North American bats since it was first reported in 2006. The causal agent of the disease is a psychrophilic filamentous fungus, Pseudogymnoascus destructans. The fungus is widely distributed in North America and Europe and has recently been found in some parts of Asia, but interestingly, no mass mortality is observed in European or Asian bats. Here we report a novel double-stranded RNA virus found in North American isolates of the fungus and show that the virus can be used as a tool to study the epidemiology of White-nose syndrome. The virus, termed Pseudogymnoascus destructans partitivirus-pa, contains 2 genomic segments, dsRNA 1 and dsRNA 2 of 1.76 kbp and 1.59 kbp respectively, each possessing a single open reading frame, and forms isometric particles approximately 30 nm in diameter, characteristic of the genus Gammapartitivirus in the family Partitiviridae. Phylogenetic analysis revealed that the virus is closely related to Penicillium stoloniferum virus S. We were able to cure P. destructans of the virus by treating fungal cultures with polyethylene glycol. Examination of 62 isolates of P. destructans including 35 from United States, 10 from Canada and 17 from Europe showed virus infection only in North American isolates of the fungus. Bayesian phylogenetic analysis using nucleotide sequences of the viral coat protein geographically clustered North American isolates indicating fungal spread followed by local adaptation of P. destructans in different regions of the United States and Canada. This is the first demonstration that a mycovirus potentially can be used to study fungal disease epidemiology., Competing Interests: The authors have declared that no competing interests exist.

The role of biotic and abiotic factors in shaping the diversity and composition of communities of plant viruses remain understudied, particularly in natural settings. In this study, we test the effects of host identity, location, and sampling year on the taxonomic composition of plant viruses in six native plant species [ Ambrosia psilostachya (Asteraceae), Vernonia baldwinii (Asteraceae), Asclepias viridis (Asclepiadaceae) , Ruellia humilis (Acanthaceae), Panicum virgatum (Poaceae) and Sorghastrum nutans (Poaceae)] from the Nature Conservancy's Tallgrass Prairie Preserve in northeastern Oklahoma. We sampled over 400 specimens of the target host plants from twenty sites (plots) in the Tallgrass Prairie Preserve over 4 years and tested them for the presence of plant viruses applying virus-like particle and double-stranded RNA enrichment methods. Many of the viral sequences identified could not be readily assigned to species, either due to their novelty or the shortness of the sequence. We thus grouped our putative viruses into operational viral taxonomic units for further analysis. Partial canonical correspondence analysis revealed that the taxonomic composition of plant viruses in the target species had a significant relationship with host species ( P value: 0.001) but no clear relation with sampling site or year. Variation partitioning further showed that host identity explained about 2-5 per cent of the variation in plant virus composition. We could not interpret the significant relationship between virus composition and host plants with respect to host taxonomy or ecology. Only six operational viral taxonomic units had over 5 per cent incidence over a 4-year period, while the remainder exhibited sporadic infection of the target hosts. This study is the first of its kind to document the dynamics of the entire range of viruses in multiple plant species in a natural setting.

Viruses are most frequently discovered because they cause disease. To expand knowledge of plant-associated viruses beyond these narrow constraints, non-cultivated plants of the Tallgrass Prairie of the United States were systematically surveyed for evidence of viruses. This report discusses putative viruses of the family Secoviridae identified by the survey. Sequence analysis suggests the presence of at least six viruses in the study site, including Bean pod mottle virus, Maize chlorotic dwarf virus, three previously undescribed viruses within the subfamily Comovirinae and one unclassifiable virus., (Copyright © 2012 Elsevier B.V. All rights reserved.)

The diversity of viruses associated with non-cultivated plants was assessed from plant samples collected in the Tallgrass Prairie Preserve of northeastern Oklahoma, USA. The samples were processed to determine the sequences of nucleic acids extracted from the virus-like particle fraction of plant homogenates. Sequences from 95 specimens of 52 plant species included those of probable origin from the genomes of plants (including retroelements), bacteria, fungi, other organisms, and viruses. Virus-like sequences were identified in sequences from 25% of the specimens, coming from 19% of the plant species. Evidence of a member of the genus Tymovirus was found in 16 specimens of 6 plant species, making it the most predominant virus associated with the sampled plants. There was evidence of the presence of more than one virus in each of six specimens.

To test the hypothesis that many viruses remain to be discovered in plants, a procedure was developed to sequence nucleic acids cloned randomly from virus-like particle fractions of plant homogenates. As a test of the efficiency of the procedure we targeted Ambrosia psilostachya, western ragweed, plants growing at the Tallgrass Prairie Preserve of northeastern Oklahoma. Amplifiable nucleic acid was found in the fractions from six of twelve specimens and sequences were characterized from four of them. Evidence was obtained for the presence of viruses belonging to two families (Caulimoviridae, Flexiviridae). Multiple viral species were found in two of the four specimens and their level within the isolated nucleic acid population varied from less than 1-37%. None of the sequences were derived from reported sequences of known viruses. Thus, the analysis of nucleic acid from virus-like particles is a useful tool to expand our knowledge of the universe of viruses to non-cultivated species.

Purpose: To evaluate the efficacy of training programmes for the village health practitioners aimed at improving primary orthopaedic and trauma care in our rural setting., Materials & Methods: Six year prospective study of training workshops in local health institutions was carried out using locally available manpower and materials., Results: After 6 years the evaluation of this programme shows a significantly improved (p < 0.05) knowledge base and working skills after completion of training workshop., Summary: To avoid unnecessary complications, effective primary health care provided by an appropriately trained person should be available at the peripheral level. This training programme seems successful in achieving this goal and hence needs adoption for wider use in Nepal.

Bed management is one of the important activities for efficient hospital management. The present study on evaluation of bed management in a rural hospital revealed that the total bed capacity could not be utilised. The turnover rate, turnover interval, bed occupancy rate and average length of stay were closely corroborating.