Analyzing Large-Scale Single-Cell RNA-Seq Data Using Coreset.

The recent boom in single-cell sequencing technologies provides valuable insights into the transcriptomes of individual cells. Through single-cell data analyses, a number of biological discoveries, such as novel cell types, developmental cell lineage trajectories, and gene regulatory networks, have been uncovered. However, the massive and increasingly accumulated single-cell datasets have also posed a seriously computational and analytical challenge for researchers. To address this issue, one typically applies dimensionality reduction approaches to reduce the large-scale datasets. However, these approaches are generally computationally infeasible for tall matrices. In addition, the downstream data analysis tasks such as clustering still take a large time complexity even on the dimension-reduced datasets. We present single-cell Coreset (scCoreset), a data summarization framework that extracts a small weighted subset of cells from a huge sparse single-cell RNA-seq data to facilitate the downstream data analysis tasks. Single-cell data analyses run on the extracted subset yield similar results to those derived from the original uncompressed data. Tests on various single-cell datasets show that scCoreset outperforms the existing data summarization approaches for common downstream tasks such as visualization and clustering. We believe that scCoreset can serve as a useful plug-in tool to improve the efficiency of current single-cell RNA-seq data analyses.

A review of the potential involvement of small RNAs in transgenerational abiotic stress memory in plants.

Crop production is increasingly threatened by the escalating weather events and rising temperatures associated with global climate change. Plants have evolved adaptive mechanisms, including stress memory, to cope with abiotic stresses such as heat, drought, and salinity. Stress memory involves priming, where plants remember prior stress exposures, providing enhanced responses to subsequent stress events. Stress memory can manifest as somatic, intergenerational, or transgenerational memory, persisting for different durations. The chromatin, a central regulator of gene expression, undergoes modifications like DNA acetylation, methylation, and histone variations in response to abiotic stress. Histone modifications, such as H3K4me3 and acetylation, play crucial roles in regulating gene expression. Abiotic stresses like drought and salinity are significant challenges to crop production, leading to yield reductions. Plant responses to stress involve strategies like escape, avoidance, and tolerance, each influencing growth stages differently. Soil salinity affects plant growth by disrupting water potential, causing ion toxicity, and inhibiting nutrient uptake. Understanding plant responses to these stresses requires insights into histone-mediated modifications, chromatin remodeling, and the role of small RNAs in stress memory. Histone-mediated modifications, including acetylation and methylation, contribute to epigenetic stress memory, influencing plant adaptation to environmental stressors. Chromatin remodeling play a crucial role in abiotic stress responses, affecting the expression of stress-related genes. Small RNAs; miRNAs and siRNAs, participate in stress memory pathways by guiding DNA methylation and histone modifications. The interplay of these epigenetic mechanisms helps plants adapt to recurring stress events and enhance their resilience. In conclusion, unraveling the epigenetic mechanisms in plant responses to abiotic stresses provides valuable insights for developing resilient agricultural techniques. Understanding how plants utilize stress memory, histone modifications, chromatin remodeling, and small RNAs is crucial for designing strategies to mitigate the impact of climate change on crop production and global food security.

Diabetic Foot Ulcers and Their Surgical Management: Our Experience at Hayatabad Medical Complex, Peshawar.

BACKGROUND: Surgeons face a therapeutic challenge while treating diabetic foot ulcers (DFUs), particularly in underdeveloped nations with limited healthcare resources and a high proportion of patients who arrive at medical institutions with advanced foot ulcers. OBJECTIVE: To assess the effectiveness of treatment in patients with DFUs and to demonstrate how early surgical intervention and appropriate bedside medical care can improve results. MATERIAL AND METHODS: This prospective study was carried out at Hayatabad Medical Complex, Peshawar, Pakistan, to assess how DFUs changed over a period between November 2021 and December 2022 at the wards and at the outpatient department of endocrinology and general surgery. A diabetic patient's foot is first screened for ulceration in the endocrinology department, and only those with active ulcers are referred to the surgical department. RESULTS: According to the Wagner classification, there were six (13.6%) cases in grade I, 11 (25%) in grade 2, 10 (22.7%) in grade 3, 13 (29.5%) in grade 4, and four (9%) in grade 5. Among comorbidities, a family history of diabetes mellitus was noted in 25 (56.8%) patients, followed by tobacco chewing and alcohol in 10 (22.7%) and hypertension in nine (20.4%) patients. CONCLUSION: Diabetes foot ulceration is the most common reason for non-traumatic lower limb amputation in people with diabetes mellitus and is a significant cause of morbidity and mortality.

Assessment of salt and drought stress on the biochemical and molecular functioning of onion cultivars.

BACKGROUND: Salt and drought stress are the main environmental constraints that limit onion growth and productivity. Türkiye is the fifth largest onion producer, whereas the stress conditions are increasing in the region, resulting in poor crop growth. METHODS AND RESULTS: A current study was conducted under greenhouse conditions according to a completely randomized design with factorial arrangements to evaluate the performance of onion cultivars. Plants were subjected to salt stress with an application of 750 mM NaCl and drought stress was applied by depriving plants of irrigation water for 20 days to measure biochemical and transcript changes. The antioxidant activities of the cultivars were quantified by using four different methods, i.e., 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) assays, cupric reducing antioxidant capacity, 2,2-Diphenyl-1-picrylhydrazyl, and ferric reducing antioxidant power (FRAP). The damage to pigments, phenolic, osmolytes, and hydrogen peroxide (H2O2) accumulation was also evaluated. Results revealed that the cultivars "Elit and Hazar" had higher H2O2, maximum damage to pigments, and least accumulation of phenolics and osmolytes under both stress conditions. The cultivar "Sampiyon" performance was better under salt stress but exhibited a poor antioxidant defensive mechanism under drought stress conditions. The remaining cultivars suggested a resilient nature with a higher accumulation of osmolytes, antioxidants and phenolics. The change in transcript levels further strengthened the response of resilient cultivars; for instance, they showed higher transcript levels of superoxide dismutase, ascorbate oxidase and transcription factors (WRKY70, NAC29). It helped alleviate the oxidative stress in tolerant cultivars and maintained the physio-biochemical functioning of the cultivars.. CONCLUSION: The results of the current study will fill the gap of missing literature in onion at biochemical and molecular levels. Additionally, resilient cultivars can effectively cope with abiotic stresses to ensure future food security.

The nexus between remittance, exchange rate and economic growth of E7 economies: Frequency domain analysis.

This study investigates the nexus between economic growth (GDP), trade openness, remittances, exchange rate, and agricultural output in E7 (Russia, Indonesia, Mexico, China, India, Brazil, and Turkey) economies, covering the data from 1990 to 2020. In the first step, we adopted the Dumitrescu and Hurlin time domain Granger causality test, which shows that economic growth (GDP) and agriculture do not have any causal relationship, not even at 3-lags. However, uni-directional causality exists between agriculture and economic growth at the first level difference. In the second step, we used Granger causality analysis in the frequency domain, presented by Croux and Reusens, showing a bivariate correlation among economic growth, trade, remittance, and agricultural output. The panel Granger causality outcome indicated that the causality between variables with various frequencies differs. Policymakers in these economies may consider these pragmatic results to formulate valuable and appropriate short-, medium-, and long-term economic strategies.

Comparing definitive unilateral cleft rhinoplasty with and without diced-cartilage alar-base augmentation: A retrospective cohort study.

This retrospective cohort study aimed to compare the long-term aesthetic outcomes and satisfaction of patients who underwent two techniques of definitive unilateral cleft rhinoplasty. The two cohorts, comprising patients with mature unilateral cleft deformity, were managed with definitive rhinoplasty, either with or without diced-cartilage alar-base and peri-alar augmentation (ABPA). Thirty patients were included in each cohort. Anthropometric measurements, complications, patient satisfaction scores, and third-party surgeon assessment scores were reviewed. In both cohorts, anthropometric parameters improved. Rhinoplasty with ABPA was the superior cohort in terms of columellar length (10.3 ± 1.0 in the cohort with ABPA, compared with 7.9 ± 0.6 in the cohort without ABPA; p < 0.001), alar-base angle (0.2 ± 0.2, compared with 4.3 ± 0.3; p < 0.001), and columellar deviation (2.5 ± 1.4, compared with 10.3 ± 2.1; p < 0.001). This cohort also had more symmetry in nostril height and nostril width (p < 0.001), a lower recurrence rate (one case compared with 22 cases; p < 0.001), a higher patient satisfaction score (p = 0.002), and a higher surgeon assessment score (p < 0.001, Cronbach's alpha = 0.706, Kendall's coefficient of concordance = 0.787). Within the limitations of this study, it appears that the described technique for augmenting the alar-base and peri-alar maxillary area is manageable, and yields consistent long-term results.

The Surface Properties of Implant Materials by Deposition of High-Entropy Alloys (HEAs).

High-entropy alloys (HEAs) contain more than five alloying elements in a composition range of 5-35% and with slight atomic size variation. Recent narrative studies on HEA thin films and their synthesis through deposition techniques such as sputtering have highlighted the need for determining the corrosion behaviors of such alloys used as biomaterials, for example, in implants. Coatings composed of biocompatible elements such as titanium, cobalt, chrome, nickel, and molybdenum at the nominal composition of Co30Cr20Ni20Mo20Ti10 were synthesized by means of high-vacuum radiofrequency magnetron (HVRF) sputtering. In scanning electron microscopy (SEM) analysis, the coating samples deposited with higher ion densities were thicker than those deposited with lower ion densities (thin films). The X-ray diffraction (XRD) results of the thin films heat treated at higher temperatures, i.e., 600 and 800 °C, revealed a low degree of crystallinity. In thicker coatings and samples without heat treatment, the XRD peaks were amorphous. The samples coated at lower ion densities, i.e., 20 µAcm-2, and not subjected to heat treatment yielded superior results in terms of corrosion and biocompatibility among all the samples. Heat treatment at higher temperatures led to alloy oxidation, thus compromising the corrosion property of the deposited coatings.

Developing future heat-resilient vegetable crops.

Climate change seriously impacts global agriculture, with rising temperatures directly affecting the yield. Vegetables are an essential part of daily human consumption and thus have importance among all agricultural crops. The human population is increasing daily, so there is a need for alternative ways which can be helpful in maximizing the harvestable yield of vegetables. The increase in temperature directly affects the plants' biochemical and molecular processes; having a significant impact on quality and yield. Breeding for climate-resilient crops with good yields takes a long time and lots of breeding efforts. However, with the advent of new omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, the efficiency and efficacy of unearthing information on pathways associated with high-temperature stress resilience has improved in many of the vegetable crops. Besides omics, the use of genomics-assisted breeding and new breeding approaches such as gene editing and speed breeding allow creation of modern vegetable cultivars that are more resilient to high temperatures. Collectively, these approaches will shorten the time to create and release novel vegetable varieties to meet growing demands for productivity and quality. This review discusses the effects of heat stress on vegetables and highlights recent research with a focus on how omics and genome editing can produce temperature-resilient vegetables more efficiently and faster.

The causal nexus between imports and economic growth in China, India and G7 countries: granger causality analysis in the frequency domain.

This research examine the causal nexus between imports and economic growth in China, India and G7 economies. We use BC granger causality analysis in the frequency domain short (temporary) and long term (permanent) causality. Our results suggested that, there is a frequency domain (high and low) proof of the bi-directional causal nexus between imports and economic growth. The imports and economic growth in most economies seem to be long-term and short-term dependent. This empirical study shows that policymakers of these big economies need to analyze the transformation in the import-economic growth causality robustness throughout the year when planning policy actions.

Assessment of Heavy Metal Accumulation in Soil and Garlic Influenced by Waste-Derived Organic Amendments.

In South Asia, the high costs of synthetic fertilizers have imposed research on alternative nutrient inputs. We aimed to identify potential trace elements (PTE) present in some organic manure that might be a source of environmental pollutions and risk to public health following consumption. The study aims to evaluate how different organic waste (poultry waste, PW; press mud, PM; and farmyard manure, FYM) influences the heavy metal migration in soil, the accumulation in garlic, and their potential health risks. Organic waste caused a higher accumulation of certain metals (Zn, Cu, Fe, and Co), whereas Mn, Cd, Cr, and Pb were in lower concentrations in soil. Amendments of soil with PM revealed a higher accumulation of Cd, Cr, Fe, and Pb, whereas PW resulted in Cu and Zn accumulation in garlic. Treatment of soil with FYM exhibited higher metal concentration of Co and Mn. An environmental hazard indices study revealed that pollution load index (PLI) was highest for Cu following treatment with PM. The health risk index (HRI) was greater for Cd following amendment with PM. Maximum daily intake of metals (DIM) was observed for Zn after treatment with PW. The Pb exhibited maximum bioconcentration factor (BCF) in PM-amended plants. Based on these findings, we concluded that garlic grown on contaminated soil with organic waste may pose serious health hazards following consumption.

Capturing spatial variability of factors affecting the water allocation plans-a geo-informatics approach for large irrigation schemes.

The livelihoods of poor people living in rural areas of Indus Basin Irrigation System (IBIS) of Pakistan depend largely on irrigated agriculture. Water duties in IBIS are mainly calculated based on crop-specific evapotranspiration. Recent studies show that ignoring the spatial variability of factors affecting the crop water requirements can affect the crop production. The objective of the current study is thus to identify the factors which can affect the water duties in IBIS, map these factors by GIS, and then develop the irrigation response units (IRUs), an area representing the unique combinations of factors affecting the gross irrigation requirements (GIR). The Lower Chenab Canal (LCC) irrigation scheme, the largest irrigation scheme of the IBIS, is selected as a case. Groundwater quality, groundwater levels, soil salinity, soil texture, and crop types are identified as the main factors for IRUs. GIS along with gamma design software GS + was used to delineate the IRUs in the large irrigation scheme. This resulted in a total of 84 IRUs in the large irrigation scheme based on similar biophysical factors. This study provided the empathy of suitable tactics to increase water management and productivity in LCC. It will be conceivable to investigate a whole irrigation canal command in parts (considering the field-level variations) and to give definite tactics for management.

Moving Beyond DNA Sequence to Improve Plant Stress Responses.

Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.

Comparative transcriptomics of drought stress response of taproot meristem region of contrasting purple carrot breeding lines supported by physio-biochemical parameters.

Carrot is one of the nutritious vegetable crops sensitive to drought stress resulting in loss of quality and yield. There are a lot of studies on detailed molecular mechanisms of drought stress response of main crops; however, very little information available on vegetables, including carrots. Hence, in this study, we investigated root transcriptome profiles from the meristematic region of two contrasting purple carrot (B7262A, drought tolerant; P1129, drought sensitive) lines under varying stress levels (85% and 70%) by using RNA-Seq technique. The morpho-physiological and biochemical response of B7262A line exhibited tolerance behavior to both DS (85% and 70%). RNA-Seq analysis revealed that 15,839 genes were expressed commonly in both carrot lines. The carrot line B7262A showed regulation of 514 genes in response to 85% DS, whereas P1129 showed differential regulation of 622 genes under 70% DS. The B7262A carrot line showed higher upregulation of transcripts that suggested its resilient behavior contrary to P1129 line. Furthermore, validation of transcript gene by qRT-PCR also confirmed the RNA-Seq analysis resulting in elevated expression levels of MYB48 transcription factor, MAPK mitogen-activated protein kinase ANP1, GER geraniol 8-hydroxylase, ABA ABA-induced in somatic embryo 3, FBOX putative F-box protein, FRO ferric reduction oxidase, and PDR probable disease resistance protein. Current study provided unprecedented insights of purple carrot lines that can be potentially exploited for the screening and development of resilient carrot.

Unraveling Sorghum Allelopathy in Agriculture: Concepts and Implications.

Allelopathy is an ecological phenomenon that involves the production and release of biomolecules from different crops, cultivated plants, and bacteria or fungi into the soil rhizosphere and impacts other organisms in the vicinity. Sorghum possesses vital allelopathic characteristics due to which it produces and releases different biomolecules from its root hairs, stems, and grains. Several studies have reported that sorghum acts as an allelopathic crop, decreasing the growth and eco-physiological attributes of surrounding plants and weeds growing simultaneously or subsequently in the field. Sorghum allelopathy has been exploited in the context of green manure, crop rotations, cover crops, and intercropping or mulching, whereas plant aqueous extracts or powder might be an alternate method of weed control. A diverse group of allelochemicals, including benzoic acid, p-hydroxybenzoic acid, vanillic acid, ferulic acid, chlorogenic acid, m-coumaric acid, p-coumaric acid, gallic acid, caffeic acid, p-hydroxibenzaldehyde, dhurrin, sorgoleone, m-hydroxybenzoic acid and protocatechuic acid, have been isolated and identified from different plant tissues of sorghum and root exudates. These allelochemicals, especially sorgoleone, have been investigated in terms of their mode(s) of action, specific activity and selectivity, release in the rhizosphere and uptake and translocation in sensitive species. The present review describes the importance of sorghum allelopathy as an ecological tool in managing weeds, highlighting the most recent advances in the allelochemicals present in sorghum, their modes of action, and their fate in the ecosystem. Further research should focus on the evaluation and selection of sorghum cultivars with high allelopathic potential, so that sorghum allelopathy can be better utilized for weed control and yield enhancement.

Frequency of non-alcoholic fatty liver disease in patients with type-2 diabetes mellitus and its associated risk factors.

OBJECTIVE: Non-Alcoholic Fatty Liver Disease (NAFLD) is emerging as a major public health problem globally especially in patients with Type-2 Diabetes mellitus (T2DM). This study aimed to assess the frequency of NAFLD in patients with T2DM and to study its associated risk factors. METHODS: This descriptive study was conducted from April 2020 to October 2020 at the Hayatabad Medical Complex, Peshawar. Adult patients with T2DM were included in the study and underwent abdominal ultrasound for the identification of NAFLD. All the relevant clinical and biochemical characteristics were measured. RESULTS: Out of 384 participants, 236 patients (61.5%) had NAFLD on ultrasound. Patients with NAFLD had higher mean BMI, higher HbA1c, increased waist circumference, raised ALT, higher triglyceride, and low HDL. Logistic regression analysis revealed a statistically significant association with central obesity (OR = 5.448, 95% CI = 1.416-20.959, p = 0.014), higher BMI (OR = 4.435, 95% CI = 2.127-9.246, p < 0.0001), higher HbA1c [> 11%] (OR = 3.602, 95% CI = 1.438-9.019, p = 0.006), and elevated ALT (OR = 3.211, 95% CI = 1.509-6.835, p = 0.002). The highest odds for NAFLD were found for hypertriglyceridemia (OR = 11.624, 95% CI = 5.405-24.998, p < 0.0001) and low HDL (OR = 11.543, 95% CI = 2.590-51.439, p = 0.001), respectively. CONCLUSIONS: High frequency of NAFLD along with its associated clinical and laboratory risk factors were revealed. This underpins the significance of screening T2DM patients for NAFLD and assessment for and modification of its associated risk factors in routine clinical practice.

Can Apparent Diffusion Coefficient Predict the Grade, Genotype, or Proliferation Index of Oligodendrogliomas.

BACKGROUND: Genetic subsets of oligodendrogliomas (OD) have distinct chromosomal and biophysical profiles. Pretherapeutic tumor grade and genotype analysis is a challenging aspect of management, with 1p/19q codeletion status and grade of oligodendroglioma among the most important considerations for clinical decision making. METHODOLOGY: Seventy-three patients with histopathological diagnosis of oligodendroglioma were selected, and their preoperative 1.5T magnetic resonance imaging (MRI) scans were reviewed through parameters including diffusion weighted image, susceptibility-weighted imaging, and apparent diffusion coefficient (ADC). These images were correlated with patients' histopathological and chromosomal testing. Tumor border irregularity, homogeneity, contrast enhancement, and other MRI characteristics were also studied. For analysis, descriptive statistics were generated, and normality was evaluated for ADC value, age, and Ki-67 tumor proliferation index. OBJECTIVES: The study aimed to determine the correlation of ADC with Ki-67, grade, and 1p/19q co-deletion in oligodendroglioma at a tertiary care hospital within a low-middle income country. RESULTS: Ki-67 tumor proliferation index was high in 33 tumors. It was found to be statistically significant (P = 0.048) with respect to ADC, showing that 1p/19q co-deleted tumors have a difference in their Ki-67 index. Ki-67 also showed a significant relationship (P < 0.05) with grade of OD. However, there was no statistically significant relationship between 1p19q chromosomal co-deletion and ADC. Linear regression was carried out as the data set was continuous. Univariate analysis showed no significant result with all P values above 0.10. CONCLUSION: Mean ADC is a viable tool to predict Ki-67 and assist prognostic clinical decisions. However, mean ADC alone cannot predict 1p/19q codeletion and tumor grades in OD. Further supplementation with other radiological modalities may provide greater yield and positive results.

The efficacy of excision followed by intralesional 5-fluorouracil and triamcinolone acetonide versus excision followed by radiotherapy in the treatment of ear keloids: A randomized control trial.

BACKGROUND: The ear is the common site for keloid formation especially in women after ear piercing. Surgery is the main stay of treatment in these lesions but there are large numbers of treatment failures in surgery alone. OBJECTIVE: The objective of this study was to compare the efficacy of post-excision intralesional 5-fluorouracil/triamcinolone acetonide (5-FU/TAC) and post-excision radiotherapy in the treatment of ear keloids. STUDY DESIGN: A randomized controlled trial. SETTING: The study was conducted from May 2014 to January 2015 at Jinnah Burn and Reconstructive Surgery Centre, Allama Iqbal Medical College, Lahore. SUBJECT & METHODOLOGY: After approval from the hospital ethical committee, 60 patients presented in the outpatient department fulfilling the inclusion criteria were selected and randomly assigned in two groups with the help of the random number table. Patients in group A had excision followed by intralesional 5-FU/TAC injections while patients of group B had excision followed by radiotherapy. Patients were assessed at 6 months after completion of treatment for efficacy (no recurrence within 6 months of treatment). RESULTS: In our study total of 60 patients completed the study, with 30 patients in each group. 7 patients (23.34%) in Group-A and 9 patients (30%) in Group-B were males while 23 patients (76.67%) in Group-A and 21 patients (70%) in Group-B were females i.e. male to female ratio is 1:2.75. Mean age was 31.8+6.48years. The comparison of frequency of efficacy in both groups showed that 73.33% (n=22) in Group-A and 43.33% (n=13) in Group-B had efficacy, p value was calculated as 0.01, showing a significant statistical difference. CONCLUSION: Excision and intralesional 5-FU/TAC is an effective treatment for keloids on the ears.

Leucopenia as presentation of sarcoidosis.

A 20-year-old male Saudi national presented initially with leucopenia and splenomegaly. The absence of other signs of disease, progressive pancytopenia and normal bone marrow examination posed a diagnostic dilemma as to the cause of hypersplenism. Subsequently, the patient had splenectomy the histopathological appearance of which was non-caseating granuloma. A high level of angiotension converting enzyme (ACE) was found in this patient. Sarcoidosis is a recognized cause of hypersplenism, and though the disease is not yet widely described in this part of the world. It is the most probable diagnosis in this patient.