Erratum: State-Resolved Mutual Neutralization of Mg

This corrects the article DOI: 10.1103/PhysRevLett.128.033401.

Bio-waste mediated synthesis of zirconium nanoparticle fuel: Energy management strategy for performance evaluation in a diesel engine.

The impact of biosynthesized zirconium nanoparticles originated from biological waste, blended in diesel fuel processed through bio-refining strategy and its combustion, emissions, and overall diesel engine performance towards safety has been examined. Different weight fractions of zirconia nanoparticles were combined with crude diesel at 10, 20, and 30 mg/L values. According to the engine tests, Zirconia (20 nm) added to pure diesel at a concentration of 30 parts per million incremented thermal efficiencies by 4.9% compared to regular diesel fuel. The average reduction in specific fuel consumption for clean diesel fuel when the engine was operating at full power was 2.9%, 3.9%, and 4.9%. Diesel smoke, hydrocarbon, CO, and NOx emissions were reduced by 13%, 20%, 25%, and 29%, respectively, when nano additives were used at a concentration of 30 ppm.Nanoparticles enhance fuel stability, overcome detonation difficulties, and avoid fouling spark plugs. The pressure within cylinder, the temperature, and the rate at which heat is released was improved when alumina nanoparticles were appended to diesel fuel. However, both the length of the combustion and further delay in ignition were cut down. The ideal concentration of zirconia nanoparticles for improving combustion, efficiency, and emissions along with safety attainment in an internal combustion engine is recorded at 30 ppm.

Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment.

BACKGROUND: RNA-seq is being increasingly adopted for gene expression studies in a panoply of non-model organisms, with applications spanning the fields of agriculture, aquaculture, ecology, and environment. For organisms that lack a well-annotated reference genome or transcriptome, a conventional RNA-seq data analysis workflow requires constructing a de-novo transcriptome assembly and annotating it against a high-confidence protein database. The assembly serves as a reference for read mapping, and the annotation is necessary for functional analysis of genes found to be differentially expressed. However, assembly is computationally expensive. It is also prone to errors that impact expression analysis, especially since sequencing depth is typically much lower for expression studies than for transcript discovery. RESULTS: We propose a shortcut, in which we obtain counts for differential expression analysis by directly aligning RNA-seq reads to the high-confidence proteome that would have been otherwise used for annotation. By avoiding assembly, we drastically cut down computational costs - the running time on a typical dataset improves from the order of tens of hours to under half an hour, and the memory requirement is reduced from the order of tens of Gbytes to tens of Mbytes. We show through experiments on simulated and real data that our pipeline not only reduces computational costs, but has higher sensitivity and precision than a typical assembly-based pipeline. A Snakemake implementation of our workflow is available at: https://bitbucket.org/project_samar/samar . CONCLUSIONS: The flip side of RNA-seq becoming accessible to even modestly resourced labs has been that the time, labor, and infrastructure cost of bioinformatics analysis has become a bottleneck. Assembly is one such resource-hungry process, and we show here that it can be avoided for quick and easy, yet more sensitive and precise, differential gene expression analysis in non-model organisms.

Intrathecal amyloid-beta oligomer administration increases tau phosphorylation in the medial temporal lobe in the African green monkey: A nonhuman primate model of Alzheimer's disease.

AIMS: An obstacle to developing new treatment strategies for Alzheimer's disease (AD) has been the inadequate translation of findings in current AD transgenic rodent models to the prediction of clinical outcomes. By contrast, nonhuman primates (NHPs) share a close neurobiology with humans in virtually all aspects relevant to developing a translational AD model. The present investigation used African green monkeys (AGMs) to refine an inducible NHP model of AD based on the administration of amyloid-beta oligomers (AßOs), a key upstream initiator of AD pathology. METHODS: AßOs or vehicle were repeatedly delivered over 4 weeks to age-matched young adult AGMs by intracerebroventricular (ICV) or intrathecal (IT) injections. Induction of AD-like pathology was assessed in subregions of the medial temporal lobe (MTL) by quantitative immunohistochemistry (IHC) using the AT8 antibody to detect hyperphosphorylated tau. Hippocampal volume was measured by magnetic resonance imaging (MRI) scans prior to, and after, intrathecal injections. RESULTS: IT administration of AßOs in young adult AGMs revealed an elevation of tau phosphorylation in the MTL cortical memory circuit compared with controls. The largest increases were detected in the entorhinal cortex that persisted for at least 12 weeks after dosing. MRI scans showed a reduction in hippocampal volume following AßO injections. CONCLUSIONS: Repeated IT delivery of AßOs in young adult AGMs led to an accelerated AD-like neuropathology in MTL, similar to human AD, supporting the value of this translational model to de-risk the clinical trial of diagnostic and therapeutic strategies.

State-Resolved Mutual Neutralization of Mg

We present experimental final-state distributions for Mg atoms formed in Mg^{+}+D^{-} mutual neutralization reactions at center-of-mass collision energies of 59±12 meV by using the merged-beams method. Comparisons with available full-quantum results reveal large discrepancies and a previously underestimated total rate coefficient by up to a factor of 2 in the 0-1 eV (<10^{4} K) regime. Asymptotic model calculations are shown to describe the process much better and we recommend applying this method to more complex iron group systems; data that is of urgent need in stellar spectral modeling.

A Survey on 5G and LPWAN-IoT for Improved Smart Cities and Remote Area Applications: From the Aspect of Architecture and Security.

Addressing the recent trend of the massive demand for resources and ubiquitous use for all citizens has led to the conceptualization of technologies such as the Internet of Things (IoT) and smart cities. Ubiquitous IoT connectivity can be achieved to serve both urban and underserved remote areas such as rural communities by deploying 5G mobile networks with Low Power Wide Area Network (LPWAN). The current architectures will not offer flexible connectivity to many IoT applications due to high service demand, data exchange, emerging technologies, and security challenges. Hence, this paper explores various architectures that consider a hybrid 5G-LPWAN-IoT and Smart Cities. This includes security challenges as well as endogenous security and solutions in 5G and LPWAN-IoT. The slicing of virtual networks using software-defined network (SDN)/network function virtualization (NFV) based on the different quality of service (QoS) to satisfy different services and quality of experience (QoE) is presented. Also, a strategy that considers the implementation of 5G jointly with Weightless-N (TVWS) technologies to reduce the cell edge interference is considered. Discussions on the need for ubiquity connectivity leveraging 5G and LPWAN-IoT are presented. In addition, future research directions are presented, including a unified 5G network and LPWAN-IoT architecture that will holistically support integration with emerging technologies and endogenous security for improved/secured smart cities and remote areas IoT applications. Finally, the use of LPWAN jointly with low earth orbit (LEO) satellites for ubiquitous IoT connectivity is advocated in this paper.

Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across sites of varying climate profiles.

BACKGROUND: The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab juveniles from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response. RESULTS: We present the first ever transcriptome assembly of S. serrata obtained from a data set containing 66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Our assembly contains many almost full-length transcripts - 5229 shrimp and 3049 fruit fly proteins have alignments that cover >80% of their sequence lengths to a contig. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat-stress response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis showed that between Cagayan and Bataan, there were 389 genes associated with 48 signaling and stress-response pathways, for which there was an effect of site in the response to heat; and between Cagayan and Bicol, there were 101 such genes affecting 8 pathways. CONCLUSION: In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.

Jointly aligning a group of DNA reads improves accuracy of identifying large deletions.

Performing sequence alignment to identify structural variants, such as large deletions, from genome sequencing data is a fundamental task, but current methods are far from perfect. The current practice is to independently align each DNA read to a reference genome. We show that the propensity of genomic rearrangements to accumulate in repeat-rich regions imposes severe ambiguities in these alignments, and consequently on the variant calls-with current read lengths, this affects more than one third of known large deletions in the C. Venter genome. We present a method to jointly align reads to a genome, whereby alignment ambiguity of one read can be disambiguated by other reads. We show this leads to a significant improvement in the accuracy of identifying large deletions (≥20 bases), while imposing minimal computational overhead and maintaining an overall running time that is at par with current tools. A software implementation is available as an open-source Python program called JRA at https://bitbucket.org/jointreadalignment/jra-src.

Combining probabilistic alignments with read pair information improves accuracy of split-alignments.

Motivation: Split-alignments provide base-pair-resolution evidence of genomic rearrangements. In practice, they are found by first computing high-scoring local alignments, parts of which are then combined into a split-alignment. This approach is challenging when aligning a short read to a large and repetitive reference, as it tends to produce many spurious local alignments leading to ambiguities in identifying the correct split-alignment. This problem is further exacerbated by the fact that rearrangements tend to occur in repeat-rich regions. Results: We propose a split-alignment technique that combats the issue of ambiguous alignments by combining information from probabilistic alignment with positional information from paired-end reads. We demonstrate that our method finds accurate split-alignments, and that this translates into improved performance of variant-calling tools that rely on split-alignments. Availability and implementation: An open-source implementation is freely available at: https://bitbucket.org/splitpairedend/last-split-pe. Supplementary information: Supplementary data are available at Bioinformatics online.

Reconstructing the demographic history of the Himalayan and adjoining populations.

The rugged topography of the Himalayan region has hindered large-scale human migrations, population admixture and assimilation. Such complexity in geographical structure might have facilitated the existence of several small isolated communities in this region. We have genotyped about 850,000 autosomal markers among 35 individuals belonging to the four major populations inhabiting the Himalaya and adjoining regions. In addition, we have genotyped 794 individuals belonging to 16 ethnic groups from the same region, for uniparental (mitochondrial and Y chromosomal DNA) markers. Our results in the light of various statistical analyses suggest a closer link of the Himalayan and adjoining populations to East Asia than their immediate geographical neighbours in South Asia. Allele frequency-based analyses likely support the existence of a specific ancestry component in the Himalayan and adjoining populations. The admixture time estimate suggests a recent westward migration of populations living to the East of the Himalaya. Furthermore, the uniparental marker analysis among the Himalayan and adjoining populations reveal the presence of East, Southeast and South Asian genetic signatures. Interestingly, we observed an antagonistic association of Y chromosomal haplogroups O3 and D clines with the longitudinal distance. Thus, we summarise that studying the Himalayan and adjoining populations is essential for a comprehensive reconstruction of the human evolutionary and ethnolinguistic history of eastern Eurasia.

Ganglioneuroma of Spinal Nerve Root: A Rare Case Mimicking Herniated Lumbar Disc and Lumbar Radiculopathy.

Ganglioneuromas are rare benign tumors arising from neuroepithelial cells. Even more rarely they involve lumbar spinal nerve roots. We report a 34-year-old male patient who presented with typical lumbar radiculopathy. He had low back pain radiating to the right lower leg with numbness. His MRI revealed a herniated disc at L5-S1 compressing the right nerve root. Surgery was planned for microdiscectomy and nerve root decompression. Right L5 hemilaminotomy was performed and the nerve root was identified. Surprisingly the nerve root was markedly inflamed and there was no obvious disc tissue herniation. Considering it to be a spinal nerve root tumor, the dura of the nerve root was opened and nerve root mass exposed. Subtotal resection was performed. Biopsy showed Ganglioneuroma. The main purpose of this article is to report such a rare case and also to review the literature.

Indian Siddis: African descendants with Indian admixture.

The Siddis (Afro-Indians) are a tribal population whose members live in coastal Karnataka, Gujarat, and in some parts of Andhra Pradesh. Historical records indicate that the Portuguese brought the Siddis to India from Africa about 300-500 years ago; however, there is little information about their more precise ancestral origins. Here, we perform a genome-wide survey to understand the population history of the Siddis. Using hundreds of thousands of autosomal markers, we show that they have inherited ancestry from Africans, Indians, and possibly Europeans (Portuguese). Additionally, analyses of the uniparental (Y-chromosomal and mitochondrial DNA) markers indicate that the Siddis trace their ancestry to Bantu speakers from sub-Saharan Africa. We estimate that the admixture between the African ancestors of the Siddis and neighboring South Asian groups probably occurred in the past eight generations (∼200 years ago), consistent with historical records.

Case Report: Robotic-Assisted Minimally Invasive Repair of a Direct Sliding Left Inguinal Hernia Containing Bladder and Colon.

A direct sliding inguinal hernia descends through the superficial inguinal ring and encroaches on nearby organ structures, such as the bladder. This type of hernia is rare with a 2-5% incidence and occurs due to a weakness within the lower abdominal wall, usually associated with advancing age, that permits the distal colon to descend into the inguinal canal. Direct sliding inguinal hernias are a rare subset of inguinal hernias that require meticulous dissection due to their incorporation of nearby organs such as the bladder or colon. Few cases report repair of these hernias laparoscopically; however, the use of a hybrid laparoscopic/open approach has not been extensively documented and it may be beneficial to explore the use of this approach in inguinal hernia repair.  We present a case of a robotic-assisted minimally invasive repair of a direct sliding inguinal hernia in an 85-year-old male. He initially presented to the emergency department with left-sided groin pain and imaging revealed he had a direct sliding inguinal hernia that incorporated the bladder wall. He was admitted to surgery for a robotic-assisted minimally invasive inguinal hernia repair with mesh. During the surgery, after seeing the extent at which the hernia sac incorporated the bladder wall, the procedure was converted to an open approach to perform the remainder of the reduction; however the robot was reintroduced for mesh placement. Post-operatively, the patient experienced mild incisional abdominal pain with return of bowel function on day four and was discharged that same day.

RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci.

BACKGROUND: As the number of genome-wide association study (GWAS) and quantitative trait locus (QTL) mappings in rice continues to grow, so does the already long list of genomic loci associated with important agronomic traits. Typically, loci implicated by GWAS/QTL analysis contain tens to hundreds to thousands of single-nucleotide polmorphisms (SNPs)/genes, not all of which are causal and many of which are in noncoding regions. Unraveling the biological mechanisms that tie the GWAS regions and QTLs to the trait of interest is challenging, especially since it requires collating functional genomics information about the loci from multiple, disparate data sources. RESULTS: We present RicePilaf, a web app for post-GWAS/QTL analysis, that performs a slew of novel bioinformatics analyses to cross-reference GWAS results and QTL mappings with a host of publicly available rice databases. In particular, it integrates (i) pangenomic information from high-quality genome builds of multiple rice varieties, (ii) coexpression information from genome-scale coexpression networks, (iii) ontology and pathway information, (iv) regulatory information from rice transcription factor databases, (v) epigenomic information from multiple high-throughput epigenetic experiments, and (vi) text-mining information extracted from scientific abstracts linking genes and traits. We demonstrate the utility of RicePilaf by applying it to analyze GWAS peaks of preharvest sprouting and genes underlying yield-under-drought QTLs. CONCLUSIONS: RicePilaf enables rice scientists and breeders to shed functional light on their GWAS regions and QTLs, and it provides them with a means to prioritize SNPs/genes for further experiments. The source code, a Docker image, and a demo version of RicePilaf are publicly available at https://github.com/bioinfodlsu/rice-pilaf.

EPHX1 gene polymorphisms in alcohol dependence and their distribution among the Indian populations.

BACKGROUND: The microsomal epoxide hydrolase is a phase II enzyme of the biotransformation. The human epoxide hydrolase 1 (EPHX1) gene lies in the chromosomal region 1q42.1 and exhibits polymorphism. Two single nucleotide polymorphisms (SNPs) have been described in the coding region of the EPHX1 gene that produces two protein variants. SUBJECTS AND METHODS: A total of 604 samples belonging to 13 Indian populations were included in this study. Based on the DSM-IV criteria, 184 individuals from Kota population were classified into alcoholism cases (100) and controls (84). Genotypes of Tyr113His and His139Arg polymorphisms in the EPHX1 gene were determined using PCR and sequencing. Associations were tested using Pearson's χ(2) test and haplotype analyses. RESULTS: We found significant association between EPHX1 gene Tyr113His polymorphism and alcoholism in the Kota population (T vs. C: OR = .615, 95% CI = .399-.949, p = .027; TT vs. CC + CT: OR = .536, 95% CI = .297-.969, p = .038). The very slow activity haplotype CA (113His-139His) was also found to be associated with alcohol dependence (p = .048). Analysis of additional populations demonstrated that the Tyr113His polymorphism significantly deviated from Hardy-Weinberg equilibrium in four populations but only one population deviated for the His139Arg locus. All populations shared the four possible two-site haplotypes. Linkage disequilibrium between these two loci was not significant in any of the population studied. CONCLUSION: EPHX1 gene polymorphisms and haplotypes are associated with an increased risk for alcoholism in the Kota population. This is the first report from India that will serve as a template for future investigations of the prevalence of EPHX1 alleles in association with various clinical entities.

Transparent wood composite prepared from two commercially important tropical timber species.

Transparent wood (TW) has garnered significant global attention due to its unique properties. In this study, TW composites were fabricated using two timber species of different density classes: Ailanthus triphysa (common name: Ailanthus wood) and Hevea brasiliensis (common name: Rubberwood). Sodium hydroxide (NaOH) and Hydrogen peroxide-based alkali method was used to modify the lignin in these veneer samples, producing a white cellulose template with a fully intact hierarchical cell structure. Subsequently, a cost-effective thermosetting unsaturated polyester resin (UPR) was infiltrated into the redesigned framework and polymerized to create rigid nanostructured transparent composites. High optical haze (of 94% and 89%) and favourable light transmittance of 59 and 55 percent were exhibited by the UPR-TW composites made from rubberwood and ailanthus wood, respectively. TW was characterised using Scanning electron microscopy and Fourier-transform infrared spectroscopy. The mechanical properties of TW were measured and compared with those of natural wood and pure-polymer. Furthermore, the anisotropic light diffusion behaviour displayed by TW in accordance with the fibre orientation indicates the utility of material as a potential light shaping device. Therefore, a cost-effective and commercially viable strategy to fabricate multipurpose TW composites using a combination of lesser-known timber species (LKTS) and UPR resin was successfully demonstrated.

Agricultural waste biomass for sustainable bioenergy production: Feedstock, characterization and pre-treatment methodologies.

The worldwide trend in energy production is moving toward circular economy systems and sustainable availability of sources. Some advanced methods support the economic development of energy production by the utilization of waste biomass, while limiting ecological effects. The use of agro waste biomass is viewed as a major alternative energy source that expressively lowers greenhouse gas emissions. Agricultural residues produced as wastes after each step of agricultural production are used as sustainable biomass assets for bioenergy production. Nevertheless, agro waste biomass needs to go through a few cyclic changes, among which biomass pre-treatment contributes to the removal of lignin and has a significant role in the efficiency and yield of bioenergy production. As a result of rapid innovation in the utilization of agro waste for biomass-derived bioenergy, a comprehensive overview of the thrilling highlights and necessary advancements, in addition to a detailed analysis of feedstock, characterization, bioconversion, and contemporary pre-treatment procedures, appear to be vital. To this end, the current status in the generation of bioenergy from agro biomass through various pre-treatment procedures was examined in this study, along with presenting relevant challenges and a perspective for future investigations.

Protein embeddings improve phage-host interaction prediction.

With the growing interest in using phages to combat antimicrobial resistance, computational methods for predicting phage-host interactions have been explored to help shortlist candidate phages. Most existing models consider entire proteomes and rely on manual feature engineering, which poses difficulty in selecting the most informative sequence properties to serve as input to the model. In this paper, we framed phage-host interaction prediction as a multiclass classification problem that takes as input the embeddings of a phage's receptor-binding proteins, which are known to be the key machinery for host recognition, and predicts the host genus. We explored different protein language models to automatically encode these protein sequences into dense embeddings without the need for additional alignment or structural information. We show that the use of embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features. The highest performance was obtained using the transformer-based protein language model ProtT5, resulting in a 3% to 4% increase in weighted F1 and recall scores across different prediction confidence thresholds, compared to using selected handcrafted sequence features.

Impact of reactivity controlled compression ignition (RCCI) mode engine operation in diesel engine powered with B20 blend of waste cooking oil biodiesel.

The purpose of this study is to conduct an experimental assessment of the impact of RCCI (reactivity regulated compression ignition) on the performance, emissions, and combustion of a CRDI engine. A fuel mix (20% biodiesel, 80% diesel, and a NaOH catalyst) is generated. The produced combination is evaluated for attributes using standards established by the American Society for Testing and Materials (ASTM). The engine research included three distinct kinds of injections: 10% Pen RCCI, 20% Pen RCCI, and 30% Pen RCCI. Increasing the injection pressure increases the brake thermal efficiency, often known as BTE. NOx emissions increased as a consequence of higher injection pressures and improved combustion. However, when the injection rate is increased, the Specific Fuel Consumption (SFC) falls. The CO2 and hydrocarbon emissions, as well as the smoke opacity values, increased as the charge increased. The resultant mixture may be utilized in a CI engine with pre-mixed ignition to improve overall engine performance as well as combustion characteristics.

Replacement gastrostomy tube causing acute pancreatitis: case series with review of literature.

CONTEXT: Percutaneous endoscopic gastrostomy (PEG) feedings are generally considered safe with few serious complications. Acute pancreatitis is a rare complication associated with replacement percutaneous endoscopic gastrostomy tubes. CASE REPORT: We report two cases of acute pancreatitis induced by migrated replacement percutaneous endoscopic gastrostomy tubes. CONCLUSIONS: Migration of a balloon into the duodenum can result in external manipulation of the ampulla of Vater thereby disturbing the flow of pancreatic secretions leading to acute pancreatitis. Recognition of this complication is important and should be included as potential etiology of acute pancreatitis in patients receiving percutaneous endoscopic gastrostomy feedings. Periodic examination and documentation of the distance of the balloon from the skin should be performed to document the position of the tubes or any inadvertent migration of the tubes. The use of Foley catheters as permanent replacement tubes should be considered medically inappropriate.