bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical and Lab profile of severe and uncomplicated malaria: A prospective study from Khuzdar Balochistan
Authors: Khan Memoona , Nisar Haider , Mushahid Nuzhat
Published: September 2021

Objectives: Khuzdar, the largest city of Southern Balochistan, is endemic for malaria with API of 6. The study was aimed at comparing the clinico-lab profile of severe and uncomplicated malaria in the region and to determine any association with age. No such study is reported in the region so far.

Methods: A prospective clinical observational study was conducted in Combined Military Hospital, Khuzdar between 2018 and 2020. A total of 210 Malaria patients, irrespective of age and gender were included. Cases were categorized into severe and uncomplicated according to WHO criteria. The clinical parameters and lab profile of severe and uncomplicated cases were compared and data was analyzed using SPSS 23.0. Categorical variables were analyzed for association of clinical features with severe malaria using Fisher exact test. Continuous variables were compared between uncomplicated and severe malaria using Mann-Whitney U –test. Statistical significance of lab parameters with type of malaria was derived using Kruskal Wallis.

Results: Uncomplicated and severe cases were 191 (91%) and 19 (9%) respectively. Severe malaria was significantly associated with jaundice, bleeding from gums, epistaxis, pallor, vomiting, respiratory distress, thrombocytopenia, low Hb, raised serum bilirubin and raised PT (p value<0.05). In children, frequency of multiple complications was significantly higher than adult patients. (75% vs 25%, p-value 0.002).Overall case fatality of severe malaria was 5.2% (1/19). However, case fatality rate was 100% in cerebral malaria.

Conclusions: Certain clinical and lab parameters can be used to predict prognosis and thus avoid adverse outcome in malaria patients.

doi: https://doi.org/10.12669/pjms.37.7.4210

How to cite this:Khan M, Nisar H, Mushahid N. Clinical and Lab profile of severe and uncomplicated malaria: A prospective study from Khuzdar Balochistan. Pak J Med Sci. 2021;37(7):---------. doi: https://doi.org/10.12669/pjms.37.7.4210

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Clinical efficacy of immunotherapy combined with chemotherapy in patients with advanced gastric cancer, its effect on nutritional status and Changes of peripheral blood T lymphocyte subsets
Authors: Li Wen-wen , Jiao Jin , Wang Zhi-yu , Wei Ya-ning , Zhang Yuan-fang
Published: September 2021

Objectives: To evaluate the clinical efficacy of immunotherapy combined with chemotherapy in patients with advanced gastric cancer and its effect on nutritional status and changes of peripheral blood T lymphocyte subsets.

Methods: Sixty patients with locally advanced gastric cancer who were admitted by Affiliated Hospital of Hebei University from March 2020 to February 2021 were enrolled and randomly divided into two groups, with 30 cases in each group. The control group was treated with FOLFOX4 chemotherapy, while the experimental group was additively treated with cindilizumab on the basis of control group. The incidence of adverse reactions, clinical efficacy, improvement of nutritional and physical status, and changes in the levels of T lymphocyte subgroups in the two groups were compared and analyzed.

Results: The total effective rate was 70% in the experimental group, which was better than 43.3% of the control group (p=0.04). The improvement rate of performance status (ECOG) score and nutritional indicators in the experimental group was significantly better than that in the control group (p<0.05). Moreover, the indicators of CD3+, CD4+, CD4+/CD8+ in the experimental group were significantly higher than those in the control group after treatment, with statistically significant differences (CD3+, p=0.01; CD4 +, p=0.02; CD4+/CD8+, p=0.01).

Conclusion: Immunotherapy combined with chemotherapy has a significant effect on locally advanced gastric cancer patients, with significant improvement in physical strength and nutritional status, significant improvement in T lymphocyte function, and no obvious adverse reactions. It is worth promoting in clinical application.

doi: https://doi.org/10.12669/pjms.37.7.4347

How to cite this:Li W, Jiao J, Wang Z, Wei Y, Zhang Y. Clinical efficacy of immunotherapy combined with chemotherapy in patients with advanced gastric cancer, its effect on nutritional status and Changes of peripheral blood T lymphocyte subsets. Pak J Med Sci. 2021;37(7):---------. doi: https://doi.org/10.12669/pjms.37.7.4347

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Evaluation of adverse effects with COVID-19 vaccination in Pakistan
Authors: Abbas Dr Sana , Abbas Beenish , Amir Sidra , Wajahat Mehreen
Published: September 2021

Objectives: Vaccinations work with different mechanisms to offer protection against disease; however, process of immunity building can cause symptoms. Therefore, this study aimed to determine the immediate side effects of COVID–19 vaccination in the Pakistani Population.

Methods: This cross-sectional analytical study was conducted at Foundation University College of Dentistry, Islamabad from February to April 2021. 0.5 mL per dose of the Covid-19 vaccine was administered to the candidates. These 205 candidates receiving vaccination were then interviewed investigating the adverse effects of the vaccine. Post-vaccination side effects were compared among categorical groups using the Chi-Square test, whereas post-vaccination side effects were compared with age using independent samples T-test. A p-value of ≤0.05 was statistically significant.

Results: Among post-vaccination side effects, fever was reported by 69 participants, while 56 of 205 reported soreness, redness, and swelling at the injection site. It was reported by 42/205 participants to have felt chills and rigor, whereas gastrointestinal disturbance and flu-like symptoms were reported in 55/205 and 28/205 participants, respectively. Younger participants were more likely to develop gastrointestinal disturbance and flu-like symptoms following vaccination as compared to older participants.

Conclusion: Malaise, headache, and fever were observed to be the most common side effects of the vaccine, moreover there was a linear relationship between manifestations of adverse effects and history of comorbidities.

doi: https://doi.org/10.12669/pjms.37.7.4522

How to cite this:Abbas S, Abbas B, Amir S, Wajahat M. Evaluation of adverse effects with COVID-19 vaccination in Pakistan. Pak J Med Sci. 2021;37(7):---------.   doi: https://doi.org/10.12669/pjms.37.7.4522

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Dynkin Games with Incomplete and Asymmetric Information
Authors: De Angelis Tiziano , Ekström Erik , Glover Kristoffer
Published: September 2021

We study the value and the optimal strategies for a two-player zero-sum optimal stopping game with incomplete and asymmetric information. In our Bayesian setup, the drift of the underlying diffusion process is unknown to one player (incomplete information feature), but known to the other one (asymmetric information feature). We formulate the problem and reduce it to a fully Markovian setup where the uninformed player optimises over stopping times and the informed one uses randomised stopping times in order to hide their informational advantage. Then we provide a general verification result that allows us to find the value of the game and players’ optimal strategies by solving suitable quasi-variational inequalities with some nonstandard constraints. Finally, we study an example with linear payoffs, in which an explicit solution of the corresponding quasi-variational inequalities can be obtained.
Morphology-dependent resonance enhanced nonlinear photoacoustic effect in nanoparticle suspension: a temporal-spatial model
Authors: Zheng Zesheng , Bindra Anivind Kaur , Jin Haoran , Sun Quqin , Liu Siyu , Zheng Yuanjin
Published: September 2021

The morphology-dependent resonances (MDRs) hotspot, ubiquity formed between the pairs of nanoparticles in close vicinity, has garnered considerable recent attention. By extending this phenomenon to pulse-laser irradiated nanoparticle suspension, we demonstrate that such collective optical/thermal enhancement can give rise to the nonlinear photoacoustic (PA) generation. In this study, a temporal-spatial analytical expression is derived to quantitatively describe the nonlinear PA signal generation from nanoparticles, incorporating the Grüneisen increase at the microscopic individual particle level and MRDs enhancement at the macroscopic suspension level. The dependence of PA nonlinearity on the critical contributors, including the laser pulse width, the particle size, and the statistical interparticle spacing, is quantitatively discussed. The theory is well validated with the finite element method (FEM) and experimentally proved with semiconducting polymer nanoparticles (SPN) suspension. This work may pave a new direction towards effective MDR based nonlinear PA contract agent design.
Architecture of photonics correlation for infrared heterodyne interferometry: demonstration of amplitude-modulation based correlation
Authors: Bourdarot Guillaume , Berger Jean-Philippe , Guillet de Chatellus Hugues
Published: September 2021

In the context of mid-infrared astronomical aperture synthesis, heterodyne interferometry has been identified as a potential solution to combine a large number of telescopes in the 10 µm–20 µm wavelength regime. In search of an alternative to costly and technologically difficult digital correlation, we have proposed to correlate wide bandwidth radio-frequency signals in the analog domain, using photonics components developed in the frame of telecommunication applications. In this paper, we propose an extension to amplitude modulation of our initial proposition, in which the encoding of the heterodyne signal was performed through phase modulation. Both schemes are compared, and an experimental demonstration of correlation between two signals using amplitude modulation is presented. Our experiment shows that this concept has important advantages over phase modulation, in particular with regard to the requirements on phase stabilization. The possibility to scale-up the photonics concept to the recombination of a large number of telescopes, and a large number of spectral channels to increase the instantaneous bandwidth coverage of infrared heterodyne interferometry, is discussed. This study shows that the necessary technological building blocks of a pathfinder instrument adaptable to existing astronomical facilities are available.
Anomalous nonlinear terahertz transmission of photoexcited carbon nanotubes
Authors: Lee Byounghwak , Mousavian Ali , Bradley Alden N. , Lee Yun-Shik
Published: September 2021

We demonstrate that free-standing multi-walled carbon nanotubes exhibit
extraordinary nonlinear terahertz responses upon optical excitation.
Terahertz transmission of the photoexcited nanotubes rises in a narrow
range of intermediate intensity with increasing intensity, while
falling in the regime of low and high intensities. A theoretical
analysis shows that the nanotube conductivity drops sharply in the
region of intermediate intensity and soars elsewhere. Field-effect
mobility and field-induced carrier multiplications are considered to
be competing processes governing the rise and fall of the
conductivity.
Unsupervised deep learning for 3D reconstruction with dual-frequency fringe projection profilometry
Authors: Fan Sizhe , Liu Shaoli , Zhang Xu , Huang Hao , Liu Wei , Jin Peng
Published: September 2021

The fringe projection profilometry (FPP) technique has been widely applied in three-dimensional (3D) reconstruction in industry for its high speed and high accuracy. Recently, deep learning has been successfully applied in FPP to achieve high-accuracy and robust 3D reconstructions in an efficient way. However, the network training needs to generate and label numerous ground truth 3D data, which can be time-consuming and labor-intensive. In this paper, we propose to design an unsupervised convolutional neural network (CNN) model based on dual-frequency fringe images to fix the problem. The fringe reprojection model is created to transform the output height map to the corresponding fringe image to realize the unsupervised training of the CNN. Our network takes two fringe images with different frequencies and outputs the corresponding height map. Unlike most of the previous works, our proposed network avoids numerous data annotations and can be trained without ground truth 3D data for unsupervised learning. Experimental results verify that our proposed unsupervised model (1) can get competitive-accuracy reconstruction results compared with previous supervised methods, (2) has excellent anti-noise and generalization performance and (3) saves time for dataset generation and labeling (3.2 hours, one-sixth of the supervised method) and computer space for dataset storage (1.27 GB, one-tenth of the supervised method).
Networks of Causal Linkage Between Eigenmodes Characterize Behavioral Dynamics of Caenorhabditis elegans
Authors: Saberski Erik , Bock Antonia K. , Goodridge Rachel , Agarwal Vitul , Lorimer Tom , Rifkin Scott A. , Sugihara George
Published: September 2021

Behavioral phenotyping of model organisms has played an important role in unravelling the complexities of animal behavior. Techniques for classifying behavior often rely on easily identified changes in posture and motion. However, such approaches are likely to miss complex behaviors that cannot be readily distinguished by eye (e.g., behaviors produced by high dimensional dynamics). To explore this issue, we focus on the model organism Caenorhabditis elegans, where behaviors have been extensively recorded and classified. Using a dynamical systems lens, we identify high dimensional, nonlinear causal relationships between four basic shapes that describe worm motion (eigenmodes, also called “eigenworms”). We find relationships between all pairs of eigenmodes, but the timescales of the interactions vary between pairs and across individuals. Using these varying timescales, we create “interaction profiles” to represent an individual’s behavioral dynamics. As desired, these profiles are able to distinguish well-known behavioral states: i.e., the profiles for foraging individuals are distinct from those of individuals exhibiting an escape response. More importantly, we find that interaction profiles can distinguish high dimensional behaviors among divergent mutant strains that were previously classified as phenotypically similar. Specifically, we find it is able to detect phenotypic behavioral differences not previously identified in strains related to dysfunction of hermaphrodite-specific neurons.
A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling
Authors: Hsu Ian S. , Strome Bob , Lash Emma , Robbins Nicole , Cowen Leah E. , Moses Alan M.
Published: September 2021

Stochastic signaling dynamics expand living cells’ information processing capabilities. An increasing number of studies report that regulators encode information in their pulsatile dynamics. The evolutionary mechanisms that lead to complex signaling dynamics remain uncharacterized, perhaps because key interactions of signaling proteins are encoded in intrinsically disordered regions (IDRs), whose evolution is difficult to analyze. Here we focused on the IDR that controls the stochastic pulsing dynamics of Crz1, a transcription factor in fungi downstream of the widely conserved calcium signaling pathway. We find that Crz1 IDRs from anciently diverged fungi can all respond transiently to calcium stress; however, only Crz1 IDRs from the Saccharomyces clade support pulsatility, encode extra information, and rescue fitness in competition assays, while the Crz1 IDRs from distantly related fungi do none of the three. On the other hand, we find that Crz1 pulsing is conserved in the distantly related fungi, consistent with the evolutionary model of stabilizing selection on the signaling phenotype. Further, we show that a calcineurin docking site in a specific part of the IDRs appears to be sufficient for pulsing and show evidence for a beneficial increase in the relative calcineurin affinity of this docking site. We propose that evolutionary flexibility of functionally divergent IDRs underlies the conservation of stochastic signaling by stabilizing selection.
Mediator complex proximal Tail subunit MED30 is critical for Mediator core stability and cardiomyocyte transcriptional network
Authors: Tan Changming , Zhu Siting , Chen Zee , Liu Canzhao , Li Yang E. , Zhu Mason , Zhang Zhiyuan , Zhang Zhiwei , Zhang Lunfeng , Gu Yusu , Liang Zhengyu , Boyer Thomas G. , Ouyang Kunfu , Evans Sylvia M. , Fang Xi
Published: September 2021

Dysregulation of cardiac transcription programs has been identified in patients and families with heart failure, as well as those with morphological and functional forms of congenital heart defects. Mediator is a multi-subunit complex that plays a central role in transcription initiation by integrating regulatory signals from gene-specific transcriptional activators to RNA polymerase II (Pol II). Recently, Mediator subunit 30 (MED30), a metazoan specific Mediator subunit, has been associated with Langer-Giedion syndrome (LGS) Type II and Cornelia de Lange syndrome-4 (CDLS4), characterized by several abnormalities including congenital heart defects. A point mutation in MED30 has been identified in mouse and is associated with mitochondrial cardiomyopathy. Very recent structural analyses of Mediator revealed that MED30 localizes to the proximal Tail, anchoring Head and Tail modules, thus potentially influencing stability of the Mediator core. However, in vivo cellular and physiological roles of MED30 in maintaining Mediator core integrity remain to be tested. Here, we report that deletion of MED30 in embryonic or adult cardiomyocytes caused rapid development of cardiac defects and lethality. Importantly, cardiomyocyte specific ablation of MED30 destabilized Mediator core subunits, while the kinase module was preserved, demonstrating an essential role of MED30 in stability of the overall Mediator complex. RNAseq analyses of constitutive cardiomyocyte specific Med30 knockout (cKO) embryonic hearts and inducible cardiomyocyte specific Med30 knockout (icKO) adult cardiomyocytes further revealed critical transcription networks in cardiomyocytes controlled by Mediator. Taken together, our results demonstrated that MED30 is essential for Mediator stability and transcriptional networks in both developing and adult cardiomyocytes. Our results affirm the key role of proximal Tail modular subunits in maintaining core Mediator stability in vivo.
Predicting drug sensitivity of cancer cells based on DNA methylation levels
Authors: Miranda Sofia P. , Baião Fernanda A. , Fleck Julia L. , Piccolo Stephen R.
Published: September 2021

Cancer cell lines, which are cell cultures derived from tumor samples, represent one of the least expensive and most studied preclinical models for drug development. Accurately predicting drug responses for a given cell line based on molecular features may help to optimize drug-development pipelines and explain mechanisms behind treatment responses. In this study, we focus on DNA methylation profiles as one type of molecular feature that is known to drive tumorigenesis and modulate treatment responses. Using genome-wide, DNA methylation profiles from 987 cell lines in the Genomics of Drug Sensitivity in Cancer database, we used machine-learning algorithms to evaluate the potential to predict cytotoxic responses for eight anti-cancer drugs. We compared the performance of five classification algorithms and four regression algorithms representing diverse methodologies, including tree-, probability-, kernel-, ensemble-, and distance-based approaches. We artificially subsampled the data to varying degrees, aiming to understand whether training based on relatively extreme outcomes would yield improved performance. When using classification or regression algorithms to predict discrete or continuous responses, respectively, we consistently observed excellent predictive performance when the training and test sets consisted of cell-line data. Classification algorithms performed best when we trained the models using cell lines with relatively extreme drug-response values, attaining area-under-the-receiver-operating-characteristic-curve values as high as 0.97. The regression algorithms performed best when we trained the models using the full range of drug-response values, although this depended on the performance metrics we used. Finally, we used patient data from The Cancer Genome Atlas to evaluate the feasibility of classifying clinical responses for human tumors based on models derived from cell lines. Generally, the algorithms were unable to identify patterns that predicted patient responses reliably; however, predictions by the Random Forests algorithm were significantly correlated with Temozolomide responses for low-grade gliomas.
A Focal Adhesion Filament Cross-correlation Kit for fast, automated segmentation and correlation of focal adhesions and actin stress fibers in cells
Authors: Hauke Lara , Narasimhan Shwetha , Primeßnig Andreas , Kaverina Irina , Rehfeldt Florian
Published: September 2021

Focal adhesions (FAs) and associated actin stress fibers (SFs) form a complex mechanical system that mediates bidirectional interactions between cells and their environment. This linked network is essential for mechanosensing, force production and force transduction, thus directly governing cellular processes like polarization, migration and extracellular matrix remodeling. We introduce a tool for fast and robust coupled analysis of both FAs and SFs named the Focal Adhesion Filament Cross-correlation Kit (FAFCK). Our software can detect and record location, axes lengths, area, orientation, and aspect ratio of focal adhesion structures as well as the location, length, width and orientation of actin stress fibers. This enables users to automate analysis of the correlation of FAs and SFs and study the stress fiber system in a higher degree, pivotal to accurately evaluate transmission of mechanocellular forces between a cell and its surroundings. The FAFCK is particularly suited for unbiased and systematic quantitative analysis of FAs and SFs necessary for novel approaches of traction force microscopy that uses the additional data from the cellular side to calculate the stress distribution in the substrate. For validation and comparison with other tools, we provide datasets of cells of varying quality that are labelled by a human expert. Datasets and FAFCK are freely available as open source under the GNU General Public License.
Optimization of factors affecting the rooting of pine wilt disease resistant Masson pine (Pinus massoniana) stem cuttings
Authors: Pan Ting , Chen Xue-lian , Hao Yan-ping , Jiang Chun-wu , Wang Song , Wang Jin-shan , Wei Qiang , Chen Shi-juan , Yu Xiao-song , Cheng Feng , Xu Liu-yi
Published: September 2021

Pine wilt disease (PWD) is a devastating disease affecting trees belonging to the genus Pinus. To control the spread of PWD in the Masson pine forest in China, PWD resistant Masson pine clones have been selected by the Anhui Academy of Forestry. However, because Masson pine is a difficult-to-root species, producing seedlings is challenging, especially from trees older than 5 years of age, which impedes the application of PWD resistant clones. In this study, we investigated the factors affecting rooting of PWD resistant clones and established a cheap, reliable, and simple method that promotes rooting. We tested the effects of three management methods, four substrates, two cutting materials, two cutting treatments, and three collection times on the rooting of cuttings obtained from 9-year-old PWD resistant clones. Rooting was observed only in stem cuttings treated with the full-light automatic spray management method. Additionally, stem cuttings showed a significantly higher rooting rate and root quality than needles cuttings. Compared with other substrates, stem cuttings planted in perlite produced the longest adventitious root and the highest total root length and lateral root number. Moreover, stem cuttings of PWD resistant clones collected in May showed a significantly higher rooting rate and root quality than those collected in June and July. Moreover, stem cuttings prepared with a horizontal cut while retaining the needles showed significantly higher rooting rate and root quality than those prepared with a diagonal cut while partly removing the needles. This study promotes the reproduction of seedlings of PWD-resistant Masson pine clones which helps control the spread of PWD, meanwhile, provides a technical reference for the propagation of mature pine trees via cuttings.
Which functional tasks present the largest deficits for patients with total hip arthroplasty before and six months after surgery? A study of the timed up-and-go test phases
Authors: Gasparutto Xavier , Gueugnon Mathieu , Laroche Davy , Martz Pierre , Hannouche Didier , Armand Stéphane
Published: September 2021

Six to eight months after total hip arthroplasty, patients only attain 80% of the functional level of control groups. Understanding which functional tasks are most affected could help reduce this deficit by guiding rehabilitation towards them. The timed up-and-go test bundles multiple tasks together in one test and is a good indicator of a patient’s overall level of function. Previously, biomechanical analysis of its phases was used to identify specific functional deficits in pathological populations. To the best of our knowledge, this analysis has never been performed in patients who have undergone total hip arthroplasty. Seventy-one total hip arthroplasty patients performed an instrumented timed up-and-go test in a gait laboratory before and six months after surgery; fifty-two controls performed it only once. Biomechanical features were selected to analyse the test’s four phases (sit-to-stand, walking, turning, turn-to-sit) and mean differences between groups were evaluated for each phase. On average, six months after surgery, patients’ overall test time rose to 80% of the mean of the control group. The walking phase was revealed as the main deficiency before and after surgery (-41 ± 47% and -22 ± 32% slower, respectively). High standard deviations indicated that variability between patients was high. On average, patients showed improved results in every phase of the timed up-and-go test six months after surgery, but residual deficits in function differed between those phases. This simple test could be appropriate for quantifying patient-specific deficits in function and hence guiding and monitoring post-operative rehabilitation in clinical settings.
Direct sequencing of measles virus complete genomes in the midst of a large-scale outbreak
Authors: Bucris Efrat , Indenbaum Victoria , Azar Roberto , Erster Oran , Haas Eric , Mendelson Ella , Zuckerman Neta S.
Published: September 2021

Measles outbreaks escalated globally despite worldwide elimination efforts. Molecular epidemiological investigations utilizing partial measles virus (MeV) genomes are challenged by reduction in global genotypes and low evolutionary rates. Greater resolution was reached using MeV complete genomes, however time and costs limit the application to numerous samples. We developed an approach to unbiasedly sequence complete MeV genomes directly from patient urine samples. Samples were enriched for MeV using filtration or nucleases and the minimal number of sequence reads to allocate per sample based on its MeV content was assessed using in-silico reduction of sequencing depth. Application of limited-resource sequencing to treated MeV-positive samples demonstrated that 1–5 million sequences for samples with high/medium MeV quantities and 10–15 million sequences for samples with lower MeV quantities are sufficient to obtain >98% MeV genome coverage and over X50 average depth. This approach enables real-time high-resolution molecular epidemiological investigations of large-scale MeV outbreaks.
Factors contributing to farm-level productivity and household income generation in coastal Bangladesh’s rice-based farming systems
Authors: Emran Shah-Al , Krupnik Timothy J. , Aravindakshan Sreejith , Kumar Virender , Pittelkow Cameron M.
Published: September 2021

Large changes have taken place in smallholder farming systems in South Asia’s coastal areas in recent decades, particularly related to cropping intensity, input availability, climate risks, and off-farm activities. However, few studies have investigated the extent to which these changes have impacted farm-level crop productivity, which is a key driver of food security and poverty in rainfed, low-input, rice-based systems. The objective of this study was to conduct an integrated assessment of variables related to socioeconomic status, farm characteristics, and crop management practices to understand the major factors influencing crop productivity and identify promising leverage points for sustainable development in coastal Bangladesh. Using a panel survey dataset of 32 variables from 502 farm households located within polder (coastal embankment) and outside polder systems during 2005–2015, we employed statistical factor analysis to characterize five independent latent factors named here asFarming Challenges,Economic Status,Crop Management Practices,Asset Endowment,and Farm Characteristics. The factorFarming Challengesexplained the most variation among households (31%), with decreases observed over time, specifically households located outside polders. Individual variables contributing to this factor included perceived cyclone severity, household distance to main roads and input-output markets, cropping intensity, and access to extension services. The most important factors for increasing crop productivity on a household and per unit area basis wereAsset EndowmentandCrop Management Practices, respectively. The former highlights the need for increasing gross cropped area, which can be achieved through greater cropping intensity, while the latter was associated with increased fertilizer, labor, and pesticide input use. Despite the importance of these factors, household poverty trajectory maps showed that changes in off-farm income had played the strongest role in improving livelihoods in this coastal area. This study can help inform development efforts and policies for boosting farm-level crop productivity, specifically through agricultural intensification (higher cropping intensity combined with appropriate and efficient use of inputs) and expanding opportunities for off-farm income as key pathways to bring smallholder households out of poverty.
Ion transport activity and optogenetics capability of light-driven Na+-pump KR2
Authors: Hososhima Shoko , Kandori Hideki , Tsunoda Satoshi P.
Published: September 2021

KR2 from marine bacteria Krokinobacter eikastus is a light-driven Na+ pumping rhodopsin family (NaRs) member that actively transports Na+ and/or H+ depending on the ionic state. We here report electrophysiological studies on KR2 to address ion-transport properties under various electrochemical potentials of Δ[Na+], ΔpH, membrane voltage and light quality, because the contributions of these on the pumping activity were less understood so far. After transient expression of KR2 in mammalian cultured cells (ND7/23 cells), photocurrents were measured by whole-cell patch clamp under various intracellular Na+ and pH conditions. When KR2 was continuously illuminated with LED light, two distinct time constants were obtained depending on the Na+ concentration. KR2 exhibited slow ion transport (τoff of 28 ms) below 1.1 mM NaCl and rapid transport (τoff of 11 ms) above 11 mM NaCl. This indicates distinct transporting kinetics of H+ and Na+. Photocurrent amplitude (current density) depends on the intracellular Na+ concentration, as is expected for a Na+ pump. The M-intermediate in the photocycle of KR2 could be transferred into the dark state without net ion transport by blue light illumination on top of green light. The M intermediate was stabilized by higher membrane voltage. Furthermore, we assessed the optogenetic silencing effect of rat cortical neurons after expressing KR2. Light power dependency revealed that action potential was profoundly inhibited by 1.5 mW/mm2 green light illumination, confirming the ability to apply KR2 as an optogenetics silencer.
Designing and validating a Markov model for hospital-based addiction consult service impact on 12-month drug and non-drug related mortality
Authors: King Caroline A. , Englander Honora , Korthuis P. Todd , Barocas Joshua A. , McConnell K. John , Morris Cynthia D. , Cook Ryan
Published: September 2021

Introduction

Addiction consult services (ACS) engage hospitalized patients with opioid use disorder (OUD) in care and help meet their goals for substance use treatment. Little is known about how ACS affect mortality for patients with OUD. The objective of this study was to design and validate a model that estimates the impact of ACS care on 12-month mortality among hospitalized patients with OUD.

Methods

We developed a Markov model of referral to an ACS, post-discharge engagement in SUD care, and 12-month drug-related and non-drug related mortality among hospitalized patients with OUD. We populated our model using Oregon Medicaid data and validated it using international modeling standards.

Results

There were 6,654 patients with OUD hospitalized from April 2015 through December 2017. There were 114 (1.7%) drug-related deaths and 408 (6.1%) non-drug related deaths at 12 months. Bayesian logistic regression models estimated four percent (4%, 95% CI = 2%, 6%) of patients were referred to an ACS. Of those, 47% (95% CI = 37%, 57%) engaged in post-discharge OUD care, versus 20% not referred to an ACS (95% CI = 16%, 24%). The risk of drug-related death at 12 months among patients in post-discharge OUD care was 3% (95% CI = 0%, 7%) versus 6% not in care (95% CI = 2%, 10%). The risk of non-drug related death was 7% (95% CI = 1%, 13%) among patients in post-discharge OUD treatment, versus 9% not in care (95% CI = 5%, 13%). We validated our model by evaluating its predictive, external, internal, face and cross validity.

Discussion

Our novel Markov model reflects trajectories of care and survival for patients hospitalized with OUD. This model can be used to evaluate the impact of other clinical and policy changes to improve patient survival.
Statins use and COVID-19 outcomes in hospitalized patients
Authors: Ayeh Samuel K. , Abbey Enoch J. , Khalifa Banda A. A. , Nudotor Richard D. , Osei Albert Danso , Chidambaram Vignesh , Osuji Ngozi , Khan Samiha , Salia Emmanuella L. , Oduwole Modupe O. , Yusuf Hasiya E. , Lasisi Oluwatobi , Nosakhare Esosa , Karakousis Petros C.
Published: September 2021

Background

There is an urgent need for novel therapeutic strategies for reversing COVID-19-related lung inflammation. Recent evidence has demonstrated that the cholesterol-lowering agents, statins, are associated with reduced mortality in patients with various respiratory infections. We sought to investigate the relationship between statin use and COVID-19 disease severity in hospitalized patients.

Methods

A retrospective analysis of COVID-19 patients admitted to the Johns Hopkins Medical Institutions between March 1, 2020 and June 30, 2020 was performed. The outcomes of interest were mortality and severe COVID-19 infection, as defined by prolonged hospital stay (≥ 7 days) and/ or invasive mechanical ventilation. Logistic regression, Cox proportional hazards regression and propensity score matching were used to obtain both univariable and multivariable associations between covariates and outcomes in addition to the average treatment effect of statin use.

Results

Of the 4,447 patients who met our inclusion criteria, 594 (13.4%) patients were exposed to statins on admission, of which 340 (57.2%) were male. The mean age was higher in statin users compared to non-users [64.9 ± 13.4 vs. 45.5 ± 16.6 years, p <0.001]. The average treatment effect of statin use on COVID-19-related mortality was RR = 1.00 (95% CI: 0.99–1.01, p = 0.928), while its effect on severe COVID-19 infection was RR = 1.18 (95% CI: 1.11–1.27, p <0.001).

Conclusion

Statin use was not associated with altered mortality, but with an 18% increased risk of severe COVID-19 infection.
Association of sleep apnea with outcomes in peripheral artery disease: Insights from the PORTRAIT study
Authors: Jelani Qurat-ul-ain , Mena-Hurtado Carlos , Gosch Kensey , Mohammed Moghniuddin , Labrosciano Clementine , Regan Christopher , Scierka Lindsey E. , Spertus John A. , Nagpal Sameer , Smolderen Kim G.
Published: September 2021

Background

Sleep apnea is a predictor of adverse cardiovascular outcome in many cardiovascular diseases but whether it is associated with worse health status outcomes or mortality in peripheral artery disease (PAD) is unknown.

Methods

PORTRAIT is an international (US, Netherlands, Australia) prospective PAD registry that consecutively enrolled patients who presented with new-onset or recent exacerbations of PAD symptoms to any of 16 vascular specialty clinics. Health status was assessed upon presentation and at 12 months with the disease-specific Peripheral Artery Questionnaire (PAQ). Higher PAQ scores indicate better health status. A sequentially-adjusted hierarchical linear regression model examined the association between sleep apnea and 1-year PAQ symptoms, quality of life, and summary scores. Five-year survival curves by comorbid sleep apnea status for US patients were compared using the log-rank test.

Results

The mean age of the 1204 PORTRAIT participants was 67.6 ± 9.4 years with 37.5% women and 8.3% (n = 100) having sleep apnea. Patients with sleep apnea were more likely to be from the US, more sedentary, and to have diabetes, obesity, coronary disease, more depressive symptoms and a history of prior peripheral interventions. Paradoxically, they also had higher ankle-brachial indices, but lower PAQ Summary scores at presentation and 12 months (41.2 ± 22.0 vs. 49. 9± 21.6 and 58.6 ± 27.9 vs. 71.3 ± 24.9, respectively, p = <0.05). The association between sleep apnea and 1-year health status persisted after multivariable adjustment, but there were no differences in all-cause mortality over 5 years (28.0% vs. 23.4%, p = 0.76).

Conclusion

In patients presenting with PAD, comorbid sleep apnea is independently associated with worse health status over time. Future studies should test whether better treatment of sleep apnea can improve the health status of patients with PAD.

Clinical trial registration

NCT01419080
Specificity and wealth of autobiographical memories in restrictive and mixed anorexic patients
Authors: Gandolphe Marie-Charlotte , Nandrino Jean-Louis , Hendrickx Marion , Willem Clémence , Cottencin Olivier , Gérardin Priscille , Guardia Dewi , Buttitta Marie , Zanini Virginie , Dodin Vincent
Published: September 2021

The reduced specificity of positive and negative autobiographical memories observed in anorexic (AN) patients may reflect a global disturbance in their emotional information processing. However, their emotional difficulties may differ according to the subtype of AN, implying possible differences in the manifestation of autobiographical memory impairments. The aims of the study were (1) to confirm the autobiographical memory deficits in AN patients in terms of specificity and wealth of memories, and (2) to compare autobiographical deficits according to the AN subtype: restrictive type (AR) or binge/purging type (AB). Ninety-five non-clinical (NC) individuals and 95 AN patients including 69 AR and 22 AB patients were administered the Williams’ and Scott’s Autobiographical Memory Test. The results confirmed a lack of specificity regardless of emotional valence in the overall AN patient group without any distinction of subtype, which was linked to the number of hospitalizations. When the AN subtype was considered, AR patients demonstrated reduced specificity for negative memories only, suggesting differences in emotional functioning or in the mechanisms underlying reduced specificity between AR and AB patients. Furthermore, the overall AN group demonstrated lower variability and complexity in their memory content than the NC group. However, this difference in the complexity of recalled memories was only found in response to negative cues. When AN subtypes were considered, AR patients showed fewer complex memories than NC individuals. Beyond a reduced specificity, AN patients also depict a poverty in the range of event recall and a difficulty in developing narrative content. The clinical implications of such autobiographical memory deficits need to be further investigated.
Construction of an evapotranspiration model and analysis of spatiotemporal variation in Xilin River Basin, China
Authors: Yu Hongbo , Cao Congming , Zhang Qiaofeng , Bao Yuhai
Published: September 2021

Surface evapotranspiration is a water exchange process between the atmosphere, biosphere, and hydrosphere. Accurate evapotranspiration estimations in arid and semi-arid regions are important for monitoring droughts and protecting the ecological environment. The main objective of this study is to build an evapotranspiration estimation model suitable for an effective scientific and objective evaluation of water consumption in the arid and semi-arid regions of the Xilin River Basin based on comprehensive parameters, including meteorological parameters, vegetation coverage, and soil water content. In this study, the community evapotranspiration model was initially constructed using field data, which was then expanded for applicability to the Xilin River Basin based on Geographic Information System technology and spatial heterogeneity characteristics of remote sensing data; both models were significant at the 0.05 level. The monthly evapotranspiration values in July during 2000–2017 and those from April to September (growing season) during the dry, normal, and wet years were calculated using the model at the basin scale. The evapotranspiration showed a generally increasing trend, which was consistent with the fluctuation trend in precipitation in July during 2000–2017. The trend curve for evapotranspiration was gentle during the growing season in dry years, but steep during wet years. The evapotranspiration was the lowest in April, with negligible spatial variations throughout the Xilin River Basin. During May–July, the evapotranspiration was higher than that in other months, in the following order: upper reaches > middle reaches > lower reaches; this was consistent with the vegetation coverage. The evapotranspiration declined and spatial variations were not evident during August–September. The results of this study provide a reference for evapotranspiration model construction and a scientific basis for evaluating regional water resources and protecting the ecological environment.
Supporting newly graduated medical doctors in managing COVID-19: An evaluation of a Massive Open Online Course in a limited-resource setting
Authors: Findyartini Ardi , Greviana Nadia , Hanum Chaina , Husin Joseph Mikhael , Sudarsono Nani Cahyani , Krisnamurti Desak Gede Budi , Rahadiani Pratiwi
Published: September 2021

Introduction

Newly graduated medical doctors in their internships are positioned to strengthen the front line in combating COVID-19. We developed a Massive Open Online Course (MOOC) to equip them with adequate knowledge for COVID-19 management. This paper aims to analyze the MOOC and evaluate participant satisfaction and increase in knowledge after completing the course.

Methods

An observational study was conducted. Quantitative data were obtained from questionnaires and pre- and post-tests. Responses to open-ended questions of the questionnaires were collected. Analysis using the Quality Reference Framework was also completed.

Results

The MOOC consisted of fundamental knowledge of COVID-19 (Part A) and further enrichment (Part B), and the content was written in the Indonesian language. A total of 3,424 and 2,462 participants completed the course in August and November 2020, respectively. Most participants agreed that the platform was easy to navigate, the design was interesting, and the content was aligned with their needs. Pre- and post-test scores in Part A’s subjects increased significantly. Factors contributing to and inhibiting usability and areas for improvement were further highlighted.

Discussion

The use of a specific quality framework facilitated a comprehensive evaluation of the MOOC’s strengths, weaknesses, and areas for future improvements. The participants’ satisfaction and pre- and post-test results showed that the current MOOC holds great potential benefit for continuing education for medical interns joining the frontliners during the pandemic. Future implementation should consider increasing the quality of learning resources, scaling up the platform and its technical supports, and enhancing organizational supports.
Proteogenomic analysis of pancreatic cancer subtypes
Authors: Kafita Doris , Nkhoma Panji , Zulu Mildred , Sinkala Musalula
Published: September 2021

Pancreatic cancer remains a significant public health problem with an ever-rising incidence of disease. Cancers of the pancreas are characterised by various molecular aberrations, including changes in the proteomics and genomics landscape of the tumour cells. Therefore, there is a need to identify the proteomic landscape of pancreatic cancer and the specific genomic and molecular alterations associated with disease subtypes. Here, we carry out an integrative bioinformatics analysis of The Cancer Genome Atlas dataset, including proteomics and whole-exome sequencing data collected from pancreatic cancer patients. We apply unsupervised clustering on the proteomics dataset to reveal the two distinct subtypes of pancreatic cancer. Using functional and pathway analysis based on the proteomics data, we demonstrate the different molecular processes and signalling aberrations of the pancreatic cancer subtypes. In addition, we explore the clinical characteristics of these subtypes to show differences in disease outcome. Using datasets of mutations and copy number alterations, we show that various signalling pathways previously associated with pancreatic cancer are altered among both subtypes of pancreatic tumours, including the Wnt pathway, Notch pathway and PI3K-mTOR pathways. Altogether, we reveal the proteogenomic landscape of pancreatic cancer subtypes and the altered molecular processes that can be leveraged to devise more effective treatments.