bluuebunny/crossref_metadata_2025 huggingface dataset:
Scoping review of the use of virtual reality in intensive care units
Authors: Hill James Edward , Twamley Jacqueline , Breed Hetty , Kenyon Roger , Casey Rob , Zhang Jennifer , Clegg Andrew
Published: November 2021

Background

A wide range of reviews have demonstrated the effectiveness and tolerability of Virtual Reality (VR) in a range of clinical areas and subpopulations. However, no previous review has explored the current maturity, acceptability, tolerability, and effectiveness of VR with intensive care patients.

Aims

To identify the range of uses of VR for intensive care patients, classify their current phase of development, effectiveness, acceptability, and tolerability.

Methods

A scoping review was conducted. A multi‐database search was undertaken (inception to January 2021). Any type of study which examined the use of VR with the target application population of intensive care patients were included. Screening, data extraction, and assessment of quality were undertaken by a single reviewer. A meta‐analysis and a descriptive synthesis were undertaken.

Results

Six hundred and forty‐seven records were identified, after duplicate removal and screening 21 studies were included (weak quality). The majority of studies for relaxation, delirium, and Post Traumatic Stress Disorder (PTSD) were at the early stages of assessing acceptability, tolerability, and initial clinical efficacy. Virtual Reality for relaxation and delirium were well‐tolerated with completion rates of target treatment of 73.6%, (95% CI:51.1%‐96%, I2 = 98.52%) 52.7% (95% CI:52.7%‐100%, I2 = 96.8%). The majority of reasons for non‐completion were due to external clinical factors. There were some potential benefits demonstrated for the use of VR for relaxation, delirium, and sleep.

Conclusion

Virtual Reality for intensive care is a new domain of research with the majority of areas of application being in the early stages of development. There is great potential for the use of VR in this clinical environment. Further robust assessment of effectiveness is required before any clinical recommendations can be made.

Relevance to Clinical Practice

Virtual reality for ICU patients is in its infancy and is not at a stage where it should be used as routine practice. However, there is early evidence to suggest that virtual reality interventions have good acceptability and tolerability in intensive care patients for relaxation, delirium, and improving sleep.
Osmotrophy of dissolved organic carbon by coccolithophores in darkness
Authors: Godrijan Jelena , Drapeau David T. , Balch William M.
Published: November 2021

The evolutionary and ecological story of coccolithophores poses questions about their heterotrophy, surviving darkness after the end‐Cretaceous asteroid impact as well as survival in the deep ocean twilight zone. Uptake of dissolved organic carbon might be an alternative nutritional strategy for supply of energy and carbon molecules.

Using long‐term batch culture experiments, we examined coccolithophore growth and maintenance on organic compounds in darkness. Radiolabelled experiments were performed to study the uptake kinetics. Pulse–chase experiments were used to examine the uptake into unassimilated, exchangeable pools vs assimilated, nonexchangeable pools.

We found that coccolithophores were able to survive and maintain their metabolism for up to 30 d in darkness, accomplishing about one cell division. The concentration dependence for uptake was similar to the concentration dependence for growth in Cruciplacolithus neohelis, suggesting that it was taking up carbon compounds and immediately incorporating them into biomass. We recorded net incorporation of radioactivity into the particulate inorganic fraction.

We conclude that osmotrophy provides nutritional flexibility and supports long‐term survival in light intensities well below threshold for photosynthesis. The incorporation of dissolved organic matter into particulate inorganic carbon, raises fundamental questions about the role of the alkalinity pump and the alkalinity balance in the sea.
Alpine dwarf shrubs show high proportions of nonfunctional xylem: Visualization and quantification of species‐specific patterns
Authors: Ganthaler Andrea , Bär Andreas , Dämon Birgit , Losso Adriano , Nardini Andrea , Dullin Christian , Tromba Giuliana , von Arx Georg , Mayr Stefan
Published: November 2021

Xylem conductive capacity is a key determinant of plant hydraulic function and intimately linked to photosynthesis and productivity, but can be impeded by temporary or permanent conduit dysfunctions. Here we show that persistent xylem dysfunctions in unstressed plants are frequent in Alpine dwarf shrubs and occur in various but species‐specific cross‐sectional patterns. Combined synchrotron micro‐computed tomography (micro‐CT) imaging, xylem staining, and flow measurements in saturated samples of six widespread Ericaceae species evidence a high proportion (19%–50%) of hydraulically nonfunctional xylem areas in the absence of drought stress, with regular distribution of dysfunctions between or within growth rings. Dysfunctions were only partly reversible and reduced the specific hydraulic conductivity to 1.38 to 3.57 ×10−4 m2 s−1 MPa−1. Decommission of inner growth rings was clearly related to stem age and a higher vulnerability to cavitation of older rings, while the high proportion of nonfunctional conduits in each annual ring needs further investigations. The lower the xylem fraction contributing to the transport function, the higher was the hydraulic efficiency of conducting xylem areas. Improved understanding of the functional lifespan of xylem elements and the prevalence and nature of dysfunctions is critical to correctly assess structure‐function relationships and whole‐plant hydraulic strategies.
Hydrogen sulphide infiltration downregulates oxidative metabolism and extends postharvest life of banana
Authors: Siddiqui M. W. , Homa F. , Lata D. , Mir H. , Aftab T. , Mishra P.
Published: November 2021

Hydrogen sulphide (H2S) has emerged as a potential regulator of plant defence against different abiotic stresses. As a climacteric fruit, banana undergoes oxidative stresses shortly after harvest, resulting in faster ripening and senescence. This work examines the effects of vacuum infiltrated H2S on ripening inhibition of banana.

Banana fruits were vacuum infiltrated with 1 mm H2S. Effects on oxidative stress markers, physiological changes, bioactive compounds and antioxidant potentials were examined during storage at 25 °C and 75–80% RH.

Results indicate that treated fruits were less affected by oxidative stress, as evident by lower accumulation of ROS (superoxide and peroxide ions), elevated phenols content and antioxidant capacity. The ripening inhibitory effects of H2S delayed chlorophyll loss and reduced ethylene and CO2 production. H2S infiltration also reduced MDA accumulation and electrolytic leakage, resulting in longer shelf life.

Vacuum infiltration with H2S had a protective effect on postharvest banana through overcoming the deleterious effect of ROS and strengthening antioxidant potential. Thus, this method could be promising for enhanced preservation of banana during storage.
A systematic meta‐analysis based review on black soldier fly (Hermetia illucens) as a novel protein source for salmonids
Authors: Weththasinghe Pabodha , Hansen Jon Øvrum , Mydland Liv Torunn , Øverland Margareth
Published: November 2021

Black soldier fly (Hermetia illucens) has gained attention as a sustainable novel protein source in fish feed due to its high nutritional value and low environmental impacts. In the past decade, effects of the use of black soldier fly in aquafeeds have widely been studied in salmonids. A meta‐analysis was conducted to compile and systematically quantify the effect of black soldier fly in diets for salmonids on growth performance and nutrient utilization. The main meta‐analysis showed that dietary inclusion of black soldier fly did not compromise the specific growth rate, feed conversion ratio, feed intake, protein digestibility and protein efficiency ratio in salmonids. A meta‐regression was conducted to explore the possible causes of variation in growth rate, feed conversion ratio and feed intake between the studies. Fish species, protein source(s) replaced and black soldier fly inclusion level were partially responsible for the variation in growth rate between the studies. The protein source(s) replaced and black soldier fly inclusion level partially explained the variation in feed conversion ratio and feed intake respectively. The sub‐data sets sorted according to the replaced protein source(s) showed that replacing fishmeal by black soldier fly decreased growth rate and feed intake in salmonids, but replacing non‐fishmeal sources improved growth rate and feed conversion. This strengthened the importance of the type of replaced protein source(s) when evaluating nutritional values of black soldier fly for salmonids. In conclusion, the present meta‐analysis showed that black soldier fly is a promising protein source for salmonid feeds.
A comparative analysis of Inspector responses to complaints about psychosocial and physical hazards
Authors: Popple Sam , Way Kïrsten , Johnstone Richard , Croucher Richard , Miller Peta
Published: November 2021

Work Health and Safety Inspectors are at the forefront of efforts to protect workers from harm from psychosocial hazards, yet the application of regulatory theory to their practice has been limited. Drawing on models of responsive regulation and strategic enforcement, we analyze extensive (N= 46,348) complaint and incident notification data from an Australian Work Health and Safety Inspectorate, to compare Inspectors' responses to psychosocial versus non‐psychosocial hazards. We found psychosocial hazards were less likely to be actioned than non‐psychosocial hazards. When they were actioned, psychosocial hazards saw more Inspector activity, but fewer enforcement notices than non‐psychosocial hazards. These findings are inconsistent with the version of responsive regulation espoused by the regulator. Our theoretical conclusion is that Weil's strategic enforcement approach is likely to offer greater possibilities for guiding future resource allocation.
A Decision Support System for Addressing Food Security in the United Kingdom
Authors: Barons Martine J. , Fonseca Thais C. O. , Davis Andy , Smith Jim Q.
Published: November 2021

This paper presents an integrating decision support system (IDSS) for food security in the United Kingdom. In ever-larger dynamic systems, such as the food system, it is increasingly difficult for decision makers (DMs) to effectively account for all the variables within the system that may influence the outcomes of interest under enactments of various candidate policies. Each of the influencing variables is likely, themselves, to be dynamic subsystems with expert domains supported by sophisticated probabilistic models. Recent increases in food poverty in the United Kingdom have raised the questions about the main drivers of food insecurity, how this may be changing over time and how evidence can be used in evaluating policy for decision support. In this context, an IDSS is proposed for household food security to allow DMs to compare several candidate policies which may affect the outcome of food insecurity at the household level.
Chromatin and regulatory differentiation between bundle sheath and mesophyll cells in maize
Authors: Dai Xiuru , Tu Xiaoyu , Du Baijuan , Dong Pengfei , Sun Shilei , Wang Xianglan , Sun Jing , Li Gang , Lu Tiegang , Zhong Silin , Li Pinghua
Published: November 2021

C4 plants partition photosynthesis enzymes between the bundle sheath (BS) and the mesophyll (M) cells for the better delivery of CO2 to RuBisCO and to reduce photorespiration. To better understand how C4 photosynthesis is regulated at the transcriptional level, we performed RNA‐seq, ATAC‐seq, ChIP‐seq and Bisulfite‐seq (BS‐seq) on BS and M cells isolated from maize leaves. By integrating differentially expressed genes with chromatin features, we found that chromatin accessibility coordinates with epigenetic features, especially H3K27me3 modification and CHH methylation, to regulate cell type‐preferentially enriched gene expression. Not only the chromatin‐accessible regions (ACRs) proximal to the genes (pACRs) but also the distal ACRs (dACRs) are determinants of cell type‐preferentially enriched expression. We further identified cell type‐preferentially enriched motifs, e.g. AAAG for BS cells and TGACC/T for M cells, and determined their corresponding transcription factors: DOFs and WRKYs. The complex interaction between cis and trans factors in the preferential expression of C4 genes was also observed. Interestingly, cell type‐preferentially enriched gene expression can be fine‐tuned by the coordination of multiple chromatin features. Such coordination may be critical in ensuring the cell type‐specific function of key C4 genes. Based on the observed cell type‐preferentially enriched expression pattern and coordinated chromatin features, we predicted a set of functionally unknown genes, e.g. Zm00001d042050 and Zm00001d040659, to be potential key C4 genes. Our findings provide deep insight into the architectures associated with C4 gene expression and could serve as a valuable resource to further identify the regulatory mechanisms present in C4 species.
Enhancing the dark side: asymmetric gain of cone photoreceptors underpins their discrimination of visual scenes based on skewness
Authors: Yedutenko Matthew , Howlett Marcus H. C. , Kamermans Maarten
Published: November 2021

Psychophysical data indicate that humans can discriminate visual scenes based on their skewness, i.e. the ratio of dark and bright patches within a visual scene. It has also been shown that at a phenomenological level this skew discrimination is described by the so‐called blackshot mechanism, which accentuates strong negative contrasts within a scene. Here, we present a set of observations suggesting that the underlying computation might start as early as the cone phototransduction cascade, whose gain is higher for strong negative contrasts than for strong positive contrasts. We recorded from goldfish cone photoreceptors and found that the asymmetry in the phototransduction gain leads to responses with larger amplitudes when using negatively rather than positively skewed light stimuli. This asymmetry in amplitude was present in the cone photocurrent, voltage response and synaptic output. Given that the properties of the phototransduction cascade are universal across vertebrates, it is possible that the mechanism shown here gives rise to a general ability to discriminate between scenes based only on their skewness, which psychophysical studies have shown humans can do. Thus, our data suggest the importance of non‐linearity of the early photoreceptor for perception. Additionally, we found that stimulus skewness leads to a subtle change in photoreceptor kinetics. For negatively skewed stimuli, the impulse response functions of the cone peak later than for positively skewed stimuli. However, stimulus skewness does not affect the overall integration time of the cone.

Key points

Humans can discriminate visual scenes based on skewness, i.e. the relative prevalence of bright and dark patches within a scene.

Here, we show that negatively skewed time‐series stimuli induce larger responses in goldfish cone photoreceptors than comparable positively skewed stimuli.

This response asymmetry originates from within the phototransduction cascade, where gain is higher for strong negative contrasts (dark patches) than for strong positive contrasts (bright patches).

Unlike the implicit assumption often contained within models of downstream visual neurons, our data show that cone photoreceptors do not simply relay linearly filtered versions of visual stimuli to downstream circuitry, but that they also emphasize specific stimulus features.

Given that the phototransduction cascade properties among vertebrate retinas are mostly universal, our data imply that the skew discrimination by human subjects reported in psychophysical studies might stem from the asymmetric gain function of the phototransduction cascade.
IDC Sensor for Low-Cost Water Quality Monitoring Applications
Authors: Mendez-Chaves Diego , Perez Manuel , Farfan Alejandro , Gerlein Eduardo
Published: November 2021

In order to properly monitor the health status of the hydrological resources of a region, in terms of water contamination, a scalable and low-cost system is necessary to map the water quality at different locations and allow the prioritization of more sophisticated and expensive monitoring campaigns on those areas where a suspicious behavior seems to be occurring. This paper presents the design and implementation process of such an IoT-based solution for low-cost and scalable water quality monitoring applications. To achieve that end, we propose the utilization of a low-cost inter-digital capacitance (IDC) sensor to characterize the conductivity of the water, a very telling parameter about the level of pollution in the water. Additionally, an embedded method to measure such sensor was designed and implemented, which considers the requirements of a portable platform: low computational capabilities, small memory and low power consumption. Our results show that an IDC sensor is capable of detecting the changes of the capacitance of the sample, and therefore mapping the changes in the conductivity of the water. Additionally, integrating an embedded measuring method is a valid option for in-situ characterization of water samples and the complete solution enables a new paradigm for water quality monitoring in large scale scenarios.
Operating Room Time Prediction: An Application of Latent Class Analysis and Machine Learning
Authors: Gañán-Cárdenas Eduard Alexander , Pemberthy-Ruiz Jorge Isaac , Rivera-Agudelo Juan Carlos , Mendoza- Arango Maria Clara
Published: November 2021

Objective: The objective of this work is to build a prediction model for Operating Room Time (ORT) to be used in an intelligent scheduling system. This prediction is a complex exercise due to its high variability and multiple influential variables. Materials and methods: We assessed a new strategy using Latent Class Analysis (LCA) and clustering methods to identify subgroups of procedures and surgeries that are combined with prediction models to improve ORT estimates. Three tree-based models are assessed, Classification and Regression Trees (CART), Conditional Random Forest (CFOREST) and Gradient Boosting Machine (GBM), under two scenarios: (i) basic dataset of predictors and (ii) complete dataset with binary procedures. To evaluate the model, we use a test dataset and a training dataset to tune parameters. Results and discussion: The best results are obtained with GBM model using the complete dataset and the grouping variables, with an operational accuracy of 57.3% in the test set. Conclusion: The results indicate the GBM model outperforms other models and it improves with the inclusion of the procedures as binary variables and the addition of the grouping variables obtained with LCA and hierarchical clustering that perform the identification of homogeneous groups of procedures and surgeries.
Identifying extreme ultraviolet lithography attenuated phase shifting mask absorber materials using effective media approximation modeling
Authors: Sejpal Rajiv , Smith Bruce
Published: November 2021

Pattern transfer in an extreme ultraviolet lithography (EUVL) system requires reflective optical elements illuminated at oblique illumination angles. This, in combination with the three-dimensional effects at the mask, is the source of the so-called mask 3D (M3D) effects that include shadowing, best focus shifts, and contrast fading. Alternative mask absorbers at lower thickness possess the ability to extenuate the M3D effects and improve overall imaging performance. An approach to recognize candidate material combinations as alternative EUVL mask absorbers through dielectric constant modeling by using methods involving Wiener bounds and effective media approximation (EMA) is presented. Using EMA, several stoichiometrically stable binary alloys of refractory metals that may serve as attenuated phase shifting mask absorbers have been studied. The optical properties and thickness of each absorber candidate alloy in a standard EUV mask stack are optimized for imaging performance. The best performing alloys are characterized through rigorous 3D image modeling of near-field intensity and phase at varied illumination angles.
Experimental investigation of dynamic lingual organ pipes with blown open tongue
Authors: Rucz Péter , Angster Judit , Miklós András
Published: November 2021

This paper presents the experimental examination of an alternative lingual organ pipe construction that uses a free tongue which, in contrast with traditional lingual organ pipes, operates in a blown open manner. A possible advantage of the construction is that it can enable changing the windchest pressure and thus, achieving an extended dynamic range while keeping a constant pitch. Three experimental pipes with diverse resonator shapes are investigated in various setups. The three pipes also demonstrate the variety of timbres obtainable by different configurations of tongues and resonators. The analysis of the measurement results shows that the pipes exhibit a very good stability of the fundamental frequency and can have a dynamic range of 15 dB. At the same time, the timbre of the sound is found to change significantly as the windchest pressure is increased. Experiments performed with damping the resonator reveal the working principle of the tongue–resonator coupling in the alternative construction. Several sound recordings are presented as multimedia file attachments enabling the subjective comparison of the pipe sounds.
Simultaneous Validation of Count-to-Activity Thresholds for Five Commonly Used Activity Monitors in Adolescent Research: A Step Toward Data Harmonization
Authors: Hayes Gráinne , Dowd Kieran , MacDonncha Ciaran , Donnely Alan
Published: November 2021

Background: Multiple activity monitors are utilized for the estimation of moderate- to vigorous-intensity physical activity in youth. Due to differing methodological approaches, results are not comparable when developing thresholds for the determination of moderate- to vigorous-intensity physical activity. This study aimed to develop and validate count-to-activity thresholds for 1.5, 3, and 6 metabolic equivalents of task in five of the most commonly used activity monitors in adolescent research. Methods: Fifty-two participants (mean age = 16.1 [0.78] years) selected and performed activities of daily living while wearing a COSMED K4b2 and five activity monitors; ActiGraph GT1M, ActiGraph wGT3X-BT, activPAL3 micro, activPAL, and GENEActiv. Receiver-operating-characteristic analysis was used to examine the area under the curve and to define count-to-activity thresholds for the vertical axis (all monitors) and the sum of the vector magnitude (ActiGraph wGT3X-BT and activPAL3 micro) for 15 s (all monitors) and 60 s (ActiGraph monitors) epochs. Results: All developed count-to-activity thresholds demonstrated high levels of sensitivity and specificity. When cross-validated in an independent group (N = 20), high levels of sensitivity and specificity generally remained (≥73.1%, intensity and monitor dependent). Conclusions: This study provides researchers with the opportunity to analyze and cross-compare data from different studies that have not employed the same motion sensors.
Visual Strategies Underpinning the Spatiotemporal Demands During Visuomotor Tasks in Predicting Ball Direction
Authors: Piras Alessandro , Timmis Matthew A. , Trofè Aurelio , Raffi Milena
Published: November 2021

We investigated gaze behavior of expert goalkeepers during the prediction of penalty kicks in different spatiotemporal constraints: penalties taken from 11 and 6 m. From 11 m, goalkeepers were more successful in predicting ball direction, with longer movement time initiation and a visual strategy with more fixations and greater saccade rates than penalties from 6 m, where they exhibited fewer fixations with higher microsaccade rates. As long as the opponent’s distance is large and time pressure low, gaze can be frequently shifted between the kicker’s body and the ball, due to the low cost of saccades. Conversely, when the objects are close, there is increased reliance on foveal and parafoveal information. In conclusion, when the spatiotemporal constraint is less severe, goalkeepers adopt a visual strategy with more fixations and small saccades. When the spatiotemporal constraint is more severe, they rely on peripheral vision to monitor kickers’ movements through the use of microsaccades.
Test–Retest Reliability of a New Device Versus a Long-Arm Goniometer to Evaluate Knee Proprioception
Authors: Tian Fei , Zhao Yaqi , Li Jixin , Wang Wenjin , Wu Danni , Li Qiang , Guo Liyun , Wang Shaobai
Published: November 2021

Context: Many methods used to evaluate knee proprioception have shortcomings that limit their use in clinical settings. Based on an inexpensive 3D camera, a new portable device was recently used to evaluate the joint position sense (JPS) of the knee joint. However, the test–retest reliability of the new method remains unclear. This study aimed to evaluate the test–retest reliability of the new device and a long-arm goniometer for assessing knee JPS, and to compare the variability of the 2 methods. Design: Prospective observational study of the test–retest reliability of knee JPS measurements. Methods: Twenty-one healthy adults were tested in 2 sessions with a 1-week interval. Three target knee flexion angles (30°, 45°, and 60°) were reproduced in each session. Target and reproduced angles were measured with both methods. Intraclass correlation coefficients, standard error of the measurement, and Bland–Altman plots were used to quantify test–retest reliability. Paired t tests were used to compare knee JPS (absolute error of the target-reproduced angle) between the methods. Results: The new device (good to excellent intraclass correlation coefficients .74–.80; standard error of the measurement 0.52°–0.61°) demonstrated better test–retest reliability than the goniometer (poor to fair intraclass correlation coefficients .23–.43; standard error of the measurement 0.89°–2.07°) and better test–retest agreement (respective mean differences for the 30°, 45°, and 60° knee angles: 0.11°, 0.13°, and 0.41° for the new system; 0.84°, 1.52°, and 1.18° for the goniometer). The measurements (absolute errors of the target-reproduced angles) with the goniometer were significantly greater than those with the new device (P < .05); the SDs of repeated measurements with the goniometer (1.50°–2.41°) were greater than with the new device (1.08°–1.38°). Conclusions: Given that the new device has good reliability and sufficient precision, it is the better alternative for evaluating knee JPS. Goniometers should be used with caution to assess knee JPS.
Dual NADPH oxidases DUOX1 and DUOX2 synthesize NAADP and are necessary for Ca
2+
signaling during T cell activation
Authors: Gu Feng , Krüger Aileen , Roggenkamp Hannes G. , Alpers Rick , Lodygin Dmitri , Jaquet Vincent , Möckl Franziska , Hernandez C. Lola C. , Winterberg Kai , Bauche Andreas , Rosche Anette , Grasberger Helmut , Kao John Y. , Schetelig Daniel , Werner René , Schröder Katrin , Carty Michael , Bowie Andrew G. , Huber Samuel , Meier Chris , Mittrücker Hans-Willi , Heeren Joerg , Krause Karl-Heinz , Flügel Alexander , Diercks Björn-Philipp , Guse Andreas H.
Published: November 2021

The enzymes DUOX1 and DUOX2 may mediate rapid and then sustained NAADP production to promote Ca
2+
signaling in T cells.
Interfacing with a receptor
Authors: Foley John F.
Published: November 2021

Distinct structural interactions determine the coupling of a single GPCR to two different G proteins.
Toxoplasma gondii
GRA28
Is Required for Placenta-Specific Induction of the Regulatory Chemokine CCL22 in Human and Mouse
Authors: Rudzki Elizabeth N. , Ander Stephanie E. , Coombs Rachel S. , Alrubaye Hisham S. , Cabo Leah F. , Blank Matthew L. , Gutiérrez-Melo Nicolás , Dubey J. P. , Coyne Carolyn B. , Boyle Jon P.
Published: November 2021

Toxoplasma gondii
is a globally ubiquitous pathogen that can cause severe disease in HIV/AIDS patients and can also cross the placenta and infect the developing fetus. We have found that placental and immune cells infected with
T. gondii
secrete significant amounts of a chemokine (called CCL22) that is critical for immune tolerance during pregnancy.
HIV Proviral Burden, Genetic Diversity, and Dynamics in Viremic Controllers Who Subsequently Initiated Suppressive Antiretroviral Therapy
Authors: Omondi F. Harrison , Sudderuddin Hanwei , Shahid Aniqa , Kinloch Natalie N. , Jones Bradley R. , Miller Rachel L. , Tsai Olivia , MacMillan Daniel , Trocha Alicja , Brockman Mark A. , Brumme Chanson J. , Joy Jeffrey B. , Liang Richard , Walker Bruce D. , Brumme Zabrina L.
Published: November 2021

HIV therapy is lifelong because integrated, replication-competent viral copies persist within long-lived cells. To cure HIV, we need to understand when these viral reservoirs form, how large and genetically diverse they are, and how long they endure.
A Histone Deacetylase, Magnaporthe oryzae RPD3, Regulates Reproduction and Pathogenic Development in the Rice Blast Fungus
Authors: Lee Song Hee , Farh Mohamed El-Agamy , Lee Jaejoon , Oh Young Taek , Cho Eunbyeol , Park Jiyeun , Son Hokyoung , Jeon Junhyun
Published: November 2021

RPD3 is an evolutionarily conserved class I histone deacetylase (HDAC) that plays a pivotal role in diverse cellular processes. In filamentous fungal pathogens, abrogation of the gene encoding RPD3 results in either lethality or severe growth impairment, making subsequent genetic analyses challenging.
Magnaporthe oryzae
is a causal agent of rice blast disease, which is responsible for significant annual yield losses in rice production.
Deep Mutational Scanning Reveals the Active-Site Sequence Requirements for the Colistin Antibiotic Resistance Enzyme MCR-1
Authors: Sun Zhizeng , Palzkill Timothy
Published: November 2021

Polymyxin antibiotics are used as last-line antibiotics in treating infections caused by multidrug-resistant pathogens. However, widespread use of polymyxins has led to the emergence of resistance.
A Bacterial Cell-Based Assay To Study SARS-CoV-2 Protein-Protein Interactions
Authors: Springstein Benjamin L. , Deighan Padraig , Grabe Grzegorz J. , Hochschild Ann
Published: November 2021

Understanding how virally encoded proteins interact with one another is essential in elucidating basic viral biology, providing a foundation for therapeutic discovery. Here, we describe the use of a versatile bacterium-based system to investigate the interactions of the protein set encoded by SARS-CoV-2, the virus responsible for the current COVID-19 pandemic.
AI4AMP: an Antimicrobial Peptide Predictor Using Physicochemical Property-Based Encoding Method and Deep Learning
Authors: Lin Tzu-Tang , Yang Li-Yen , Lu I-Hsuan , Cheng Wen-Chih , Hsu Zhe-Ren , Chen Shu-Hwa , Lin Chung-Yen
Published: November 2021

Antimicrobial peptides (AMPs) are innate immune components that have aroused a great deal of interest among drug developers recently, as they may become a substitute for antibiotics. New candidates need to fight antibiotic resistance, while discovering novel AMPs through wet-lab screening approaches is inefficient and expensive.
Ectopic pregnancy with etonogestrel implant
Authors: Rodrigues Marta Luísa , Branco Rute , Landim Elsa
Published: November 2021

The etonogestrel implant is the most effective contraceptive available. We report a case of ectopic pregnancy in a woman who had an etonogestrel implant inserted 15 months ago and the effective concentration of the implant was within normal limits.
Autoamputated ovarian mass causing a partial bowel obstruction in an infant with literature review
Authors: Engwall-Gill Abigail , Dougherty Danielle , Rausch Savannah , Perrone Erin
Published: November 2021

An autoamputated ovary (AO) is an extremely rare circumstance with a few reports in the literature. We present a case of a 3-month-old girl with a history of vague abdominal symptoms as well as a known ovarian mass, which was initially suspected to be benign and regressing. On laparoscopy for pain and obstructive symptoms, she was found to have an AO. The pathology was consistent with necrotic and torsed ovarian tissue with superimposed infection and possibly a cystic non-malignant teratoma. AOs are thought to originate from a torsion and are typically diagnosed incidentally. This is an interesting case of an AO causing a partial small bowel obstruction.
Complete heart block in neonatal lupus: a forgotten cause of fetal bradycardia
Authors: Bin Sakviseth , Heng Rathmony , IM Sethikar
Published: November 2021

The most common cause of congenital heart block (CHB) is neonatal lupus, an acquired autoimmune disease caused by transplacental transfer of maternal antibodies to the fetus. A full-term female neonate was admitted to neonatal intensive care unit for severe bradycardia with stable haemodynamics. The mother, showing no clinical symptoms or any particular history, was transferred to our tertiary centre for profound fetal bradycardia. At birth, the infant’s ECG showed a third-degree atrioventricular block and echocardiography was normal. Cardiac neonatal lupus was confirmed with positive maternal anti-Ro antibodies. Under close monitoring, the infant tolerated the bradycardia well (median 67 beats per minute (bpm)) and was discharged on day 6 of life. There was no indication for pacemaker, but she would be on regular follow-up with a paediatric cardiologist. This article holds an important insight as it is the first confirmed case of autoimmune CHB in Cambodia in which the mother’s antibody was found only after diagnosis on the neonate.
Treponema pallidum PCR testing for diagnosis of mucocutaneous ulcers suspicious for syphilis
Authors: Junejo Muhammad Hyder , Collery Mark , Whitlock Gary , McOwan Alan , Tittle Victoria , Nugent Diarmuid
Published: November 2021

Background

Primary syphilis is characterised by the appearance of an ulcerated lesion (chancre) on the anogenital or oral mucosa from which Treponema pallidum DNA may be detectable by PCR. Serological tests for syphilis may be non-reactive in early infection, even after the appearance of a chancre. We reviewed the use of a multiplex-PCR (M-PCR) test to determine the added value of T. pallidum DNA detection in the management of individuals presenting with mucocutaneous ulceration at a sexual health service in central London.

Methods

We performed a cross-sectional analysis of all individuals with detectable T. pallidum DNA from September 2019 to April 2020. Electronic patient records were reviewed and concomitant results for treponemal serology and/or rapid plasma reagin (RPR) extracted, along with demographic data, history of syphilis and indices of sexual behaviour including number of sexual partners contacted. Any subsequent treponemal serology and RPR results were also reviewed.

Results

M-PCR swab specimens were performed in 450 individuals, of whom 63 (14%) had detectable T. pallidum DNA; 60 of 63 (95%) were gay or bisexual men and 11 of 63 (17%) were living with HIV. A history of treated syphilis was present in 17 of 63 (27%). Same-day treponemal serology/RPR testing was performed in 58 of 63 (92%) patients. Of the 58 who had same-day syphilis serology/RPR, 9 (16%) had their syphilis infection confirmed by treponemal DNA PCR alone. A total of 165 partners were traced as contacts of infection, of whom 25 (15%) were contacts of individuals diagnosed by M-PCR testing alone.

Conclusion

In individuals with T. pallidum PCR-positive lesions, around one in six in our cohort were negative on standard diagnostic serological tests for syphilis. Treponemal DNA testing is an important addition to serological assays in individuals with mucocutaneous ulceration who are at risk of recent syphilis infection and facilitates early diagnosis and contact tracing.
Paeonol reduces IL-β production by inhibiting the activation of nucleotide oligomerization domain-like receptor protein-3 inflammasome and nuclear factor-κB in macrophages
Authors: Chen Gang , Guo Tingwang , Yang Lin
Published: November 2021

Interleukin-1β, a key cytokine in gouty inflammation, is precisely regulated by the NLRP3 inflammasome and NF-κB. Our previous study demonstrated that paeonol suppressed IL-1β production in rats with monosodium urate (MSU)-induced arthritis. Whether NLRP3 inflammasome or NF-κB is responsible for the anti-inflammatory effect of paeonol remains unclear. In this study, J774A.1 cells induced by lipopolysaccharide (LPS) plus MSU, was used to investigate the effect of paeonol on NLRP3 inflammasome activation, and J774A.1 cells induced by LPS alone were used to investigate the effect of paeonol on NF-κB activation. In J774A.1 cells induced by LPS plus MSU, paeonol decreased the levels of IL-1β and caspase-1 and reduced the MSU-induced interaction of pro-caspase-1 and apoptosis-associated speck-like protein containing caspase recruitment domain (ASC), but did not affect the levels of pro-IL-1β and pro-caspase-1. In J774A.1 cells induced by LPS alone, paeonol reduced the levels of IL-1β, NLRP3, p-IKK, p-IκBα, and p-p65, but did not affect ASC levels. Paeonol also promoted the content of IκBα and retained more p65 in the cytoplasm. Furthermore, paeonol reduced the DNA-binding activity of p65 and lowered the levels of p-JNK, p-ERK, and p-p38. These results suggest that paeonol inhibits IL-1β production by inhibiting the activation of NLRP3 inflammasome, NF-κB, and MAPK signaling pathways.
Evaluation of unprotected and rumen-protected L-carnitine in vitro and in vivo
Authors: Zheng Lin , Han Rui , Jiang Wei , Chen Long , Yu Wei , Zhong Wei-guang , Wei Bing-dong
Published: November 2021

This study aimed to evaluate the effectiveness of unprotected and rumen-protected L-carnitine through in vitro tests, rumen degradation tests, and in vivo tests. Twelve rumen-fistulated crossbred rams with similar body weights of 55 ± 3.6 kg and ages of 3 ± 0.2 yr old were divided into three treatment groups in a 3 × 3 Latin square design, G1 (basal diet with no additives), G2 (unprotected L-carnitine), or G3 (rumen-protected L-carnitine). Ruminal fluid and blood samples were collected before morning feeding on the last day of each experimental period (21 d). The percentage of L-carnitine remaining in the simulated rumen and abomasum and rumen increased with the increase in the wall material ratio (P < 0.05). L-carnitine supplementation decreased the plasma urea nitrogen concentration in the sheep (P < 0.05). G3 resulted in higher glutathione peroxidase (GSH-Px) and superoxide dismutase (SOD) activities as well as higher total antioxidant capacity (T-AOC) and lower malondialdehyde (MDA) concentrations in plasma than G1, and the difference was significant among the groups (P < 0.01). Thus, L-carnitine in the rumen could be protected by encapsulation for a certain time. Unprotected and rumen-protected L-carnitine supplementation effectively enhanced the antioxidant capacity of sheep, and the antioxidant capacity of sheep supplemented with rumen-protected L-carnitine was higher than that of sheep supplemented with unprotected L-carnitine.
Network Pharmacology Analysis to Explore the Pharmacological Mechanism of Effective Chinese Medicines in Treating Metastatic Colorectal Cancer using Meta-Analysis Approach
Authors: Zhu Ying , Yu Jieru , Zhang Kai , Feng Yuqian , Guo Kaibo , Sun Leitao , Ruan Shanming
Published: November 2021

The role of traditional Chinese medicine (TCM) on treatment of metastatic colorectal cancer (mCRC) remains controversial, and its active components and potential targets are still unclear. This study mainly aimed to assess the efficacy and safety of TCM in mCRC treatment through meta-analysis and explore the effective components and potential targets based on the network pharmacology method. We systematically searched PubMed, EMBASE, Cochrane, CBM, WanFang, and CNKI database for randomized controlled trials (RCTs) comparing the treatment of mCRC patients with and without TCM. A meta-analysis using RevMan 5.4 was conducted. In total, 25 clinical trials were analyzed, and the result demonstrated that TCM was closely correlated with the improved OS (HR: 0.63; 95% CI: 0.52–0.76; [Formula: see text] < 0.00001) and PFS (HR: 0.73; 95% CI: 0.61–0.88; [Formula: see text] = 0.0010). Then, high-frequency Chinese herbs from the prescriptions extracted from the trails included in the OS meta-analysis were counted to construct a core-effective prescription. The TCMSP database was used to retrieve the active chemical components and predict herb targets. The Genecards, OMIM, Disgenet, DrugBank, and TTD database were searched for colorectal cancer targets. R-package was used to construct the Component-Target (C-T) network based on the intersection genes. Further, we extracted hub genes from C-T network and performed functional enrichment and pathway analysis. Finally, the C-T network showed 120 herb and disease co-target genes, and the most important top 10 active components were: Quercetin, Luteolin, Wogonin, Kaempferol, Nobiletin, Baicalein, Licochalcone A, Naringenin, Isorhamnetin, and Acacetin. The first 20 hub genes were extracted: CDKN1A, CDK1, CDK2, E2F1, CDK4, PCNA, RB1, CCNA2, MAPK3, CCND1, CCNB1, JUN, MAPK1, RELA, FOS, MAPK8, STAT3, MAPK14, NR3C1, and MYC. Thus, effective Chinese herb components may inhibit the mCRC by targeting multiple biological processes of the above hub genes.
Multi-scalar field cosmological model and possible solutions using Noether symmetry approach
Authors: Mondal Santu , Bhaumik Roshni , Dutta Sourav , Chakraborty Subenoy
Published: November 2021

In this work, a cosmological model is considered having two scalar fields minimally coupled to gravity with a mixed kinetic term. The model is characterized by the coupling function and the potential function which are assumed to depend on one of the scalar fields. Instead of choosing these functions phenomenologically here, they are evaluated assuming the existence of Noether symmetry. By appropriate choice of a point transformation in the augmented space, one of the variables in the Lagrangian becomes cyclic and the evolution equations become much simpler to have solutions. Finally, the solutions are analyzed from cosmological view point.
Diagnosing Evolution of Cloud Cluster via Spatio-temporal Trace Analysis
Authors: Ruan Li , Jiao Yunpeng , Lin Tingyu , Xiao Limin , Min-Allah Nasro , Ren Lei
Published: November 2021

To analyze inner-enterprise cloud cluster performance, the role of workload analysis is of paramount interest to system designers. However, the ever-evolving nature of inner-enterprise cloud platforms such as diversity and spatio-temporal nature of workloads makes evolution diagnosing a challenging task. In this paper, we propose MuCoTrAna-Inner, an evolution diagnosing approach for a large-scale cloud data center based on comparative spatio-temporal trace analysis. Moreover, we present a case study on two representative big traces: Alibaba 2017 trace, and Alibaba 2018 trace. Novel quantitative findings along with the performance bottleneck inferences and recommendations based on workload analysis are provided. Our multifaceted analyses of the traces and new findings not only reveal interesting insights that are of interest to system designers and administrators, but also establish a new view to diagnosing the evolution of inner-enterprise cloud cluster based on trace analysis.
Total vertex-edge domination in graphs: Complexity and algorithms
Authors: Singhwal Nitisha , Reddy Palagiri Venkata Subba
Published: November 2021

Let [Formula: see text] be a simple, undirected and connected graph. A vertex [Formula: see text] of a simple, undirected graph [Formula: see text]-dominates all edges incident to at least one vertex in its closed neighborhood [Formula: see text]. A set [Formula: see text] of vertices is a vertex-edge dominating set of [Formula: see text], if every edge of graph [Formula: see text] is [Formula: see text]-dominated by some vertex of [Formula: see text]. A vertex-edge dominating set [Formula: see text] of [Formula: see text] is called a total vertex-edge dominating set if the induced subgraph [Formula: see text] has no isolated vertices. The total vertex-edge domination number [Formula: see text] is the minimum cardinality of a total vertex-edge dominating set of [Formula: see text]. In this paper, we prove that the decision problem corresponding to [Formula: see text] is NP-complete for chordal graphs, star convex bipartite graphs, comb convex bipartite graphs and planar graphs. The problem of determining [Formula: see text] of a graph [Formula: see text] is called the minimum total vertex-edge domination problem (MTVEDP). We prove that MTVEDP is linear time solvable for chain graphs and threshold graphs. We also show that MTVEDP can be approximated within approximation ratio of [Formula: see text]. It is shown that the domination and total vertex-edge domination problems are not equivalent in computational complexity aspects. Finally, an integer linear programming formulation for MTVEDP is presented.
Direction-Aware User Recommendation Based on Asymmetric Network Embedding
Authors: Zhou Sheng , Wang Xin , Ester Martin , Li Bolang , Ye Chen , Zhang Zhen , Wang Can , Bu Jiajun
Published: November 2021

User recommendation aims at recommending users with potential interests in the social network. Previous works have mainly focused on the undirected social networks with symmetric relationship such as friendship, whereas recent advances have been made on the asymmetric relationship such as the following and followed by relationship. Among the few existing direction-aware user recommendation methods, the random walk strategy has been widely adopted to extract the asymmetric proximity between users. However, according to our analysis on real-world directed social networks, we argue that the asymmetric proximity captured by existing random walk based methods are insufficient due to the inbalance in-degree and out-degree of nodes.

To tackle this challenge, we propose InfoWalk, a novel informative walk strategy to efficiently capture the asymmetric proximity solely based on random walks. By transferring the direction information into the weights of each step, InfoWalk is able to overcome the limitation of edges while simultaneously maintain both the direction and proximity. Based on the asymmetric proximity captured by InfoWalk, we further propose the qualitative (DNE-L) and quantitative (DNE-T) directed network embedding methods, capable of preserving the two properties in the embedding space. Extensive experiments conducted on six real-world benchmark datasets demonstrate the superiority of the proposed DNE model over several state-of-the-art approaches in various tasks.