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Objectives: Dengue emerged as a significant health threat in the endemic regions in recent years. However, inconsistent diagnostic accuracy in sequential dengue infections necessitate improved testing methods to ensure effective management of dengue cases. Here, we evaluated a portable, rapid, and sensitive molecular assay - Reverse Transcriptase Recombinase Polymerase Amplification Assay (RT-RAA) utilizing a mobile suitcase laboratory to detect infections in suspected dengue cases in Bangladesh., Method: 364 suspected dengue patients were enrolled in the study. Dengue cases were confirmed by a positive result from any of the four tests NS1 RDT, IgM RDT, qRT-PCR and RT-RAA assay. IgG RDT was performed to differentiate between primary and secondary dengue infections., Results: Of 364 suspected cases, 320 were confirmed dengue cases, with 55.94% classified as primary and 44.06% as secondary infections. Laboratory results showed comparable positivity rates between RT-RAA(78.8%) and NS1 RDT(77.1%) in primary dengue, followed by qRT-PCR(57.5%) and IgM RDT(12.8%). RT-RAA demonstrated superior positivity rates in secondary dengue(76.6%), surpassing RT-PCR(60.3%), NS1 RDT(27%), and IgM RDT (24.8%). Combining RT-RAA with NS1 RDT detected infections in 89.95% primary and 81.56% secondary dengue., Conclusion: The findings suggest complementing RT-RAA to NS1 RDT could significantly improve dengue detection rate, particularly for secondary infections., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Particle picking in cryo-electron tomograms (cryo-ET) is crucial for in situ structure detection of macro-molecules and protein complexes. The traditional template-matching-based approaches for particle picking suffer from template-specific biases and have low throughput. Given these problems, learning-based solutions are necessary for particle picking. However, the paucity of annotated data for training poses substantial challenges for such learning-based approaches. Moreover, preparing extensively annotated cryo-ET tomograms for particle picking is extremely time-consuming and burdensome. Addressing these challenges, we present TomoPicker, an annotation-efficient particle-picking approach that can effectively pick particles when only a minuscule portion (∼ 0.3 - 0.5%) of the total particles in a cellular cryo-ET dataset is provided for training. TomoPicker regards particle picking as a voxel classification problem and solves it with two different positive-unlabeled learning approaches. We evaluated our method on a benchmark cryo-ET dataset of eukaryotic cells, where we observed about 30% improvement by TomoPicker against the most recent state-of-the-art annotation efficient learning-based picking approaches.

The aerobic electron transfer chain builds a proton gradient by proton coupled electron transfer reactions through a series of proteins. Complex I is the first enzyme in the sequence. Here transfer of two electrons from NADH to quinone yields four protons pumped from the membrane N- (negative, higher pH) side to the P- (positive, lower pH) side. Protons move through three linear antiporter paths, with a few amino acids and waters providing the route; and through the E-channel, a complex of competing paths, with clusters of interconnected protonatable residues. Proton loading sites (PLS) transiently bind protons as they are transported from N- to P-compartments. PLS can be individual residues or extended clusters of residues. The program MCCE uses Monte Carlos sampling to analyze the E-channel proton binding in equilibrium with individual Molecular Dynamics snapshots from trajectories of Thermus thermuphillus Complex I in the apo, quinone and quinol bound states. At pH 7, the five E-channel subunits (Nqo4, Nqo7, Nqo8, Nqo10, and Nqo11) take >25,000 protonation microstates, each with different residues protonated. The microstate explosion is tamed by analyzing interconnected clusters of residues along the proton transfer paths. A proton is bound and released from a cluster of five coupled residues on the protein N-side and to six coupled residues in the protein center. Loaded microstates bind protons to sites closer to the P-side in the forward pumping direction. MCCE microstate analysis identifies strongly coupled proton binding amongst individual residues in the two PLS clusters., Competing Interests: Declaration of competing interest Marilyn Gunner reports financial support was provided by National Science Foundation. Marilyn Gunner reports financial support was provided by DOE. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

This work focused on removing iron with oxalic acid from red clay samples collected from Kapasia Upazila, Gazipur District, Bangladesh. To characterize the red clay, the study employed several techniques: particle size analysis, WDXRF (wavelength-dispersive X-ray fluorescence), AAS (atomic absorption spectroscopy), XRD (X-ray diffraction), TGA (thermogravimetric analysis), and FESEM (field emission scanning electron microscopy). Additionally, leaching experiments were conducted with varying concentrations of oxalic acid, temperatures and times. After leaching, the red clay composition changed significantly: SiO₂ increased from 53.6 % to 63.13 %, Fe₂O₃ decreased from 17.1 % to 3.64 %, Al₂O₃ remained relatively stable at 18 %-18.22 %, and other oxides showed minor variations. 78.71 % of the iron was removed at optimal leaching conditions (1.0 M oxalic acid, 100 °C, 150 min, and 250 rpm). Mineralogically, the red clay samples are composed of illite, kaolinite, quartz, feldspar, hematite and chlorite. Thermal analysis showed significant weight loss at temperatures between 300 and 600 °C. Ceramic trials were conducted at firing temperatures of 900 °C and 1100 °C to evaluate the mechanical properties of tiles. The results obtained showed significant improvements in red clay quality for ceramics. Being a low-cost and eco-friendly process, this becomes a very prominent alternative to conventional iron removal techniques and helps produce high-quality ceramic tiles, contributing towards economic growth in Bangladesh., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Arsenic (As) contamination in groundwater is emerging as a significant global concern, posing serious risks to the safety of drinking water and public health. To understand the release mechanisms, mobilization processes, spatial distribution, and probabilistic health risks of As in western Bangladesh, forty-seven samples were collected and analyzed using an atomic absorption spectrometer (AAS). The As concentrations in groundwater ranged from 1.97 to 697.4 μg L⁻ 1 (mean: 229.9), significantly exceeding recommended levels. The dominant hydrochemistry of As-enriched groundwater was Ca-Mg-HCO₃, with the primary sources of arsenic in groundwater being the dissolution of arsenic-bearing minerals in sediment and the recharge of aquifers from the Ganges River Basin. The assessment using the Entropy Water Quality Index revealed that the groundwater is unsuitable for drinking, with 89.36% (n = 42) of the samples surpassing the WHO's limit for arsenic. Rock-water interactions, including calcite dissolution and silicate weathering within the confined aquifer, predominantly influenced hydrochemical properties. The significant relationships among Fe, Mn, and As indicate that the reductive dissolution of FeOOH and/or MnOOH considerably contributes to the release of As from sediment into groundwater. Geochemical modeling analysis revealed that siderite and rhodochrosite precipitate into aquifer solids, suggesting a weak to moderate relationship among As, Fe, and Mn. The long residence time of groundwater, combined with the presence of a clayey aquitard, likely controls the mobilization of arsenic in the aquifer. For the first time, Monte Carlo simulations have been used in arsenic-prone areas to assess the severity of arsenic contamination in western Bangladesh. The analysis indicates that out of 100,000 people, 10 may develop cancer as a result of drinking arsenic-contaminated water, with children being more susceptible than adults., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Objectives: As post kala-azar Dermal Leishmaniasis (PKDL) threatens the success of the Visceral Leishmaniasis (VL) elimination initiative, we aimed to investigate the PKDL burden, including an active search for PKDL in leprosy-negative skin lesion cases. We also investigated their health-seeking behavior and perceived level of stigma., Methods: This was a cross-sectional survey among inhabitants in the VL-endemic villages of the five most VL-endemic upazilas. VL experts trained medical officers in Upazila Health Complexes (UHCs) and leprosy facilities in PKDL management. Frontline workers conducted house-to-house surveys, referring PKDL suspects to designated centers. Data analysis involved Epi Info version 7 and IBM SPSS Statistics 25., Results: Among 472,435 screened individuals, 4022 had past VL (0.85 %). Among the screened population, 82 were PKDL suspects, and 62 PKDL cases were confirmed. The overall PKDL burden was 1.3 (95 % CI: 1.0-1.7) in the 10,000 population in the endemic villages. Male predominance and macular form of PKDL were observed. Thirty-nine PKDL patients perceived stigma of different levels. Only 27 of 62 (44 %) had received PKDL treatment. Medicine's unavailability and side effects were a major reason behind treatment interruption. Active screening among 137 leprosy-negative PKDL suspects yielded 10 (7.3 %) PKDL cases., Conclusion: The existence of PKDL cases in the VL endemic areas is a concern as those are inter-epidemic reservoirs. As per the WHO roadmap, the PKDL burden must be reduced by 70 % and 100 %, respectively, by 2026 and 2030. NKEP can take the current burden of 1.3 per 10,000 people in VL endemic villages as a baseline. Integrating active case detection for PKDL in leprosy hospitals and screening centers is feasible and worth deploying nationwide., Competing Interests: Declaration of competing interest The authors have no conflicts of interest associated with the material presented in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Cryogenic Electron Tomography (CryoET) is a useful imaging technology in structural biology that is hindered by its need for manual annotations, especially in particle picking. Recent works have endeavored to remedy this issue with few-shot learning or contrastive learning techniques. However, supervised training is still inevitable for them. We instead choose to leverage the power of existing 2D foundation models and present a novel, training-free framework, CryoSAM. In addition to prompt-based single-particle instance segmentation, our approach can automatically search for similar features, facilitating full tomogram semantic segmentation with only one prompt. CryoSAM is composed of two major parts: 1) a prompt-based 3D segmentation system that uses prompts to complete single-particle instance segmentation recursively with Cross-Plane Self-Prompting, and 2) a Hierarchical Feature Matching mechanism that efficiently matches relevant features with extracted tomogram features. They collaborate to enable the segmentation of all particles of one category with just one particle-specific prompt. Our experiments show that CryoSAM outperforms existing works by a significant margin and requires even fewer annotations in particle picking. Further visualizations demonstrate its ability when dealing with full tomogram segmentation for various subcellular structures. Our code is available at: https://github.com/xulabs/aitom.

In the delta region of Bangladesh, Sonneratia apetala , also known as Keora and mangrove apple, is widely recognized for its dual role as a source of both food and medicine. Seasonal S. apetala fruits were gathered from Hatiya, Noakhali, in October 2021. The samples were segregated into pericarps and seeds, then fractionated into methanol segments. The anti-proliferative activities of these samples against lung A549 cells were evaluated using the Trypan blue exclusion method. Additionally, High-Performance Liquid Chromatography (HPLC) was employed to quantify phenolic compounds, while standard protocols facilitated the identification of specific phytochemical constituents. Chemical profiling via Gas Chromatography-Mass Spectrometry (GC-MS) and the isolation and detection of bioactive compounds through column chromatography and Nuclear Magnetic Resonance (NMR) analysis were undertaken. The methanol fractions of the seeds and pericarp were found to contain carbohydrates, tannins, flavonoids, steroids, alkaloids, glycosides, and terpenoids, with the absence of saponins and anthraquinones. Notably, the anti-proliferative effect demonstrated statistical significance at a concentration of 300 μg/mL for both extracts. Furthermore, HPLC analysis identified and quantified six polyphenols: catechin hydrate, (-)-epicatechin, rutin hydrate, trans -ferulic acid, trans -cinnamic acid, myricetin, and kaempferol, with the following concentrations: 46.65 and 12.72; 349.29 and 140.39; 5.26 and 33.06; 10.35 and 29.28; ND and 11.93; and 10.03 and 7.90 mg/100 g in the methanol fraction of the seed and pericarp, respectively. GC-MS analysis of S. apetala fruit revealed five notable compounds with significant peak areas (%): 2-methyltetracosane, tetratetracontane, heptacosane, 1-chloro-2-hexyl-1-octanol, and phenol, 3,5-bis(1,1-dimethylethyl), exhibiting peak areas of 43.96, 35.8, and 15.95, respectively. Meanwhile, the notable peak in S. apetala seeds was 1,3-benzenedicarboxylic acid, bis(2-ethylhexyl) ester, with a peak area (%) of 100. These compounds are known for their anticancer and antioxidant properties. Therefore , S. apetala , particularly its seeds and fruits, shows promising potential for development into dietary supplements and functional foods., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier Ltd.)

Tripartite resistance nodulation and cell division multidrug efflux pumps span the periplasm and are a major driver of multidrug resistance among Gram-negative bacteria. The periplasm provides a distinct environment between the inner and outer membranes of Gram-negative bacteria. Cations, such as Mg 2+ , become concentrated within the periplasm and, in contrast to the cytoplasm, its pH is sensitive to conditions outside the cell. Here, we reveal an interplay between Mg 2+ and pH in modulating the dynamics of the periplasmic adaptor protein, AcrA, and its function within the prototypical AcrAB-TolC multidrug efflux pump from Escherichia coli . In the absence of Mg 2+ , AcrA becomes increasingly plastic within acidic conditions, but when Mg 2+ is bound this is ameliorated, resulting in domain specific organisation in neutral to weakly acidic regimes. We establish a unique histidine residue directs these structural dynamics and is essential for sustaining pump efflux activity across acidic, neutral, and alkaline conditions. Overall, we propose Mg 2+ conserves the structural mobility of AcrA to ensure optimal AcrAB-TolC function within rapid changing environments commonly faced by the periplasm during bacterial infection and colonization. This work highlights that Mg 2+ is an important mechanistic component in this pump class and possibly across other periplasmic lipoproteins., Competing Interests: Competing interests The authors declare no competing interests.

Reliable separation of circulating tumor cells from blood cells is crucial for early cancer diagnosis and prognosis. Many conventional microfluidic platforms take advantage of the size difference between particles for their separation, which renders them impractical for sorting overlapping-sized cells. To address this concern, a hybrid inertial-dielectrophoretic microfluidic chip is proposed in this work for continuous and single-stage separation of lung cancer cell line A549 cells from white blood cells of overlapping size. The working mechanism of the proposed spiral microchannel embedded with planar interdigitated electrodes is validated against the experimental results. A numerical investigation is carried out over a range of flow conditions and electric field intensity to determine the separation efficiency and migration characteristics of the cell mixture. The results demonstrate the unique capability of the proposed microchannel to achieve high-throughput separation of cells at low applied voltages in both vertical and lateral directions. A significant lateral separation distance between the CTCs and the WBCs has been achieved, which allows for high-resolution and effective separation of cells. The separation resolution can be controlled by adjusting the strength of the applied electric field. Furthermore, the results demonstrate that the lateral separation distance is maximum at a voltage termed the critical voltage, which increases with the increase in the flow rate. The proposed microchannel and the developed technique can provide valuable insight into the development of a tunable and robust medical device for effective and high-throughput separation of cancer cells from the WBCs., (© 2024 The Authors. Biotechnology Progress published by Wiley Periodicals LLC on behalf of American Institute of Chemical Engineers.)

Saltwater intrusion in the coastal areas of Bangladesh is a prevalent phenomenon. However, it is not conducive to activities such as irrigation, navigation, fish spawning and shelter, and industrial usage. The present study analyzed 45 water samples collected from 15 locations in coastal areas during three seasons: monsoon, pre-monsoon, and post-monsoon. The aim was to comprehend the seasonal variation in physicochemical parameters, including water temperature, pH, electrical conductivity (EC), salinity, total dissolved solids (TDS), hardness, and concentrations of Na+, K+, Mg2+, Ca2+, Fe2+, HCO3-, PO43-, SO42-, and Cl-. Additionally, parameters essential for agriculture, such as soluble sodium percentage (SSP), sodium absorption ratio (SAR), magnesium absorption ratio (MAR), residual sodium carbonate (RSC), Kelly's ratio (KR), and permeability index (PI), were examined. Their respective values were found to be 63%, 16.83 mg/L, 34.92 mg/L, 145.44 mg/L, 1.28 mg/L, and 89.29%. The integrated water quality index was determined using entropy theory and principal component analysis (PCA). The resulting entropy water quality index (EWQI) and SAR of 49.56% and 63%, respectively, indicated that the samples are suitable for drinking but unsuitable for irrigation. These findings can assist policymakers in implementing the Bangladesh Deltaplan-2100, focusing on sustainable land management, fish cultivation, agricultural production, environmental preservation, water resource management, and environmental protection in the deltaic areas of Bangladesh. This research contributes to a deeper understanding of seasonal variations in the hydrochemistry and water quality of coastal rivers, aiding in the comprehension of salinity intrusion origins, mechanisms, and causes., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Uddin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The quality of life (QoL) of cancer patients is of paramount concern due to the enduring effects of chemotherapy on the physical, emotional, spiritual, and social aspects of life. This study aims to examine the factors influencing QoL among cancer patients. A cross-sectional analysis encompassing 200 chemotherapy patients aged 18 and above was conducted, using self-reported surveys and clinical records. The results indicate higher social wellbeing and lower physical well-being scores. Significantly, patients in joint families, with income above Rs25,000, limited pre-diagnosis check-ups, over four chemotherapy cycles, showed better QoL. Engaging diversions like art and internet usage alleviated worries. Conversely, comorbidities correlated with lower FACT-G scores. QoL is still compromised, even with the developments of advanced cancer treatments. Managing mental, emotional, social, and physical health is vital. Future research should focus on evidence-based policies, innovative strategies, psychiatric assessments, mindfulness interventions, and exploring the impact of social interactions on QoL, aiming to enhance the wellbeing of newly diagnosed cancer patients.

Groundwater is a significant water resource for drinking and irrigation in Satkhira district, Bangladesh. The depletion of groundwater resources and deterioration in its quality are the results of the confluence of factors such as industrialization, intensive irrigation, and rapid population growth. For this reason, this study focused on the evaluation of tubewell water of six unions of Kaligonj upazila in Satkhira district, which is situated in the coastal southwest part of Bangladesh. Major and trace elemental concentrations were assimilated into positive matrix factorization (PMF) to identify potential sources and their respective contributions. Principal component analysis (PCA) revealed that groundwater salinization and manmade activities were the primary causes of heavy metals in the coastal groundwater. Its average pH value was found to be 7.5, while Dissolved oxygen, Total dissolved solids, salinity, and conductivity, with values ranging from 1.18 to 7.38 mg/L, 0.5-4.88 g/L, 0.4-5%, and 0.95 to 8.56 mS/cm, respectively. The total hardness average value was 561.7 mg/L, classified into the very hard water categories, which is why 90% of the tubewell water samples were unfit for household purposes. All samples had an excessive level of arsenic present. The iron concentration of fifteen (15) samples crossed the standard limit according to WHO 2011 value. Around 63% of the samples were of the Na + -K + -Cl - -SO 4 2- type, and about 72% were sodium-potassium and alkali types. 98% of samples were covered in chloride and bicarbonate. The findings showed that 45.83% of the groundwater samples had negative Chloroalkaline index (CAIs), while 54.16% had positive. The permeability index (PI) was an average of 73%, and residual sodium carbonate (RSC) averaged 260.2 mg/L, and the findings clearly showed that 80% of the samples weren't appropriate for irrigation. According to the sodium adsorption ratio (SAR) value, 65% of the samples fell into the unsuitable category. These calculations indicated a high overall salinity hazard in the study area, which may be caused by the intrusion of sea water given that the study area is close to the coastal region. Findings compared to standards revealed that the majority of the samples were deemed unfit for drinking and irrigation purposes. Hence, additional attention must be paid to this area to ensure the availability of drinkable water and to preserve sustainable farming practices., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Eleven trace metals (Cd, Cr, Fe, Mn, Cu, Ni, Co, Zn, As, Pb, and Ag) in sediments of Bangladesh's ship breaking area were measured by an atomic absorption spectrometer to determine origin, contamination extent, spatial distributions, and associated ecological and human health hazards. This study found considerable quantities of Pb, Cd, Mn, Zn, and Cu when compared with standards and high levels of Pb, Cd, Zn, Cu, As, and Ag contamination according to pollution evaluation indices. Different indices indicate most of the sampling sites were highly polluted. However, spatial distribution maps indicate that trace metals were predominantly deposited in the northern and southern region. The ecological risk index revealed that Cd has the highest while Pb and As had moderate risk. Based on the health index values, Zn for both adults and children were higher than the safe limit while Mn, Pb, Cr, As, Fe, Cu, Ni, and Co for children were close to the threshold. The mean total carcinogenic risk values of Cr, As, and Ni for children and Ni for adults exceeded the permissible threshold. The cancer risk possibilities were further assessed using Monte Carlo simulation. Most trace metals have anthropogenic origins, which were attributed to ship breaking activities., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

In plants and algae, the primary antenna protein bound to photosystem II is light-harvesting complex II (LHCII), a pigment-protein complex that binds eight chlorophyll (Chl) a molecules and six Chl b molecules. Chl a and Chl b differ only in that Chl a has a methyl group (-CH 3 ) on one of its pyrrole rings, while Chl b has a formyl group (-CHO) at that position. This blue-shifts the Chl b absorbance relative to Chl a . It is not known how the protein selectively binds the right Chl type at each site. Knowing the selection criteria would allow the design of light-harvesting complexes that bind different Chl types, modifying an organism to utilize the light of different wavelengths. The difference in the binding affinity of Chl a and Chl b in pea and spinach LHCII was calculated using multiconformation continuum electrostatics and free energy perturbation. Both methods have identified some Chl sites where the bound Chl type ( a or b ) has a significantly higher affinity, especially when the protein provides a hydrogen bond for the Chl b formyl group. However, the Chl a sites often have little calculated preference for one Chl type, so they are predicted to bind a mixture of Chl a and b . The electron density of the spinach LHCII was reanalyzed, which, however, confirmed that there is negligible Chl b in the Chl a -binding sites. It is suggested that the protein chooses the correct Chl type during folding, segregating the preferred Chl to the correct binding site.