bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute kidney injury in critical COVID-19: a multicenter cohort analysis in seven large hospitals in Belgium
Authors: Schaubroeck Hannah , Vandenberghe Wim , Boer Willem , Boonen Eva , Dewulf Bram , Bourgeois Camille , Dubois Jasperina , Dumoulin Alexander , Fivez Tom , Gunst Jan , Hermans Greet , Lormans Piet , Meersseman Philippe , Mesotten Dieter , Stessel Björn , Vanhoof Marc , De Vlieger Greet , Hoste Eric 
Published: July 2022

Abstract
Background
Acute kidney injury (AKI) has been reported as a frequent complication of critical COVID-19. We aimed to evaluate the occurrence of AKI and use of kidney replacement therapy (KRT) in critical COVID-19, to assess patient and kidney outcomes and risk factors for AKI and differences in outcome when the diagnosis of AKI is based on urine output (UO) or on serum creatinine (sCr).

Methods
Multicenter, retrospective cohort analysis of patients with critical COVID-19 in seven large hospitals in Belgium. AKI was defined according to KDIGO within 21 days after ICU admission. Multivariable logistic regression analysis was used to explore the risk factors for developing AKI and to assess the association between AKI and ICU mortality.

Results
Of 1286 patients, 85.1% had AKI, and KRT was used in 9.8%. Older age, obesity, a higher APACHE II score and use of mechanical ventilation at day 1 of ICU stay were associated with an increased risk for AKI. After multivariable adjustment, all AKI stages were associated with ICU mortality. AKI was based on sCr in 40.1% and UO in 81.5% of patients. All AKI stages based on sCr and AKI stage 3 based on UO were associated with ICU mortality. Persistent AKI was present in 88.6% and acute kidney disease (AKD) in 87.6%. Rapid reversal of AKI yielded a better prognosis compared to persistent AKI and AKD. Kidney recovery was observed in 47.4% of surviving AKI patients.

Conclusions
Over 80% of critically ill COVID-19 patients had AKI. This was driven by the high occurrence rate of AKI defined by UO criteria. All AKI stages were associated with mortality (NCT04997915).
ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics
Authors: Hao Yajing , Zhang Shuyang , Shao Changwei , Li Junhui , Zhao Guofeng , Zhang Dong-Er , Fu Xiang-Dong 
Published: July 2022

AbstractTwo-dimensional high-throughput data have become increasingly common in functional genomics studies, which raises new challenges in data analysis. Here, we introduce a new statistic called Zeta, initially developed to identify global splicing regulators from a two-dimensional RNAi screen, a high-throughput screen coupled with high-throughput functional readouts, and ZetaSuite, a software package to facilitate general application of the Zeta statistics. We compare our approach with existing methods using multiple benchmarked datasets and then demonstrate the broad utility of ZetaSuite in processing public data from large-scale cancer dependency screens and single-cell transcriptomics studies to elucidate novel biological insights.
Development of a highly efficient prime editor 2 system in plants
Authors: Li Juan , Chen Like , Liang Jing , Xu Rongfang , Jiang Yingli , Li Yizhen , Ding Jian , Li Min , Qin Ruiying , Wei Pengcheng 
Published: July 2022

AbstractLow efficiency has seriously restricted the application of prime editing (PE) systems in plants. In this study, we develop an enhanced plant prime editor 2 system, enpPE2, by stacking various optimization strategies, including updating the PE architecture to PEmax and expressing engineered pegRNA with a structured motif under the control of a composite promoter. In T0 rice plants, enpPE2 exhibits editing frequencies of 64.58% to 77.08%, which are much higher than the frequencies with unmodified pPE2. Our results indicate that the enpPE2 system provides a robust and powerful tool for the precise modification of plant genomes.
Effectiveness and cost-effectiveness of text messages with or without endowment incentives for weight management in men with obesity (Game of Stones): study protocol for a randomised controlled trial
Authors: Macaulay Lisa , O’Dolan Catriona , Avenell Alison , Carroll Paula , Cotton Seonaidh , Dombrowski Stephan , Elders Andrew , Goulao Beatriz , Gray Cindy , Harris Fiona M. , Hunt Kate , Kee Frank , MacLennan Graeme , McDonald Matthew David , McKinley Michelle , Skinner Rebecca , Torrens Claire , Tod Martin , Turner Katrina , van der Pol Marjon , Hoddinott Pat 
Published: July 2022

Abstract
Background
Obesity increases the risk of type 2 diabetes, heart disease, stroke, mobility problems and some cancers, and its prevalence is rising. Men engage less than women in existing weight loss interventions. Game of Stones builds on a successful feasibility study and aims to find out if automated text messages with or without endowment incentives are effective and cost-effective for weight loss at 12 months compared to a waiting list comparator arm in men with obesity.

Methods
A 3-arm, parallel group, assessor-blind superiority randomised controlled trial with process evaluation will recruit 585 adult men with body mass index of 30 kg/m2 or more living in and around three UK centres (Belfast, Bristol, Glasgow), purposively targeting disadvantaged areas. Intervention groups: (i) automated, theory-informed text messages daily for 12 months plus endowment incentives linked to verified weight loss targets at 3, 6 and 12 months; (ii) the same text messages and weight loss assessment protocol; (iii) comparator group: 12 month waiting list, then text messages for 3 months. The primary outcome is percentage weight change at 12 months from baseline. Secondary outcomes at 12 months are as follows: quality of life, wellbeing, mental health, weight stigma, behaviours, satisfaction and confidence. Follow-up includes weight at 24 months. A health economic evaluation will measure cost-effectiveness over the trial and over modelled lifetime: including health service resource-use and quality-adjusted life years. The cost-utility analysis will report incremental cost per quality-adjusted life years gained. Participant and service provider perspectives will be explored via telephone interviews, and exploratory mixed methods process evaluation analyses will focus on mental health, multiple long-term conditions, health inequalities and implementation strategies.

Discussion
The trial will report whether text messages (with and without cash incentives) can help men to lose weight over 1 year and maintain this for another year compared to a comparator group; the costs and benefits to the health service; and men’s experiences of the interventions. Process analyses with public involvement and service commissioner input will ensure that this open-source digital self-care intervention could be sustainable and scalable by a range of NHS or public services.

Trial registration
ISRCTN 91974895. Registered on 14/04/2021.
Concurrent molecular characterization of sand flies and Leishmania parasites by amplicon-based next-generation sequencing
Authors: Nasereddin Abedelmajeed , Ereqat Suheir , Al-Jawabreh Amer , Taradeh Mohamad , Abbasi Ibrahim , Al-Jawabreh Hanan , Sawalha Samer , Abdeen Ziad 
Published: July 2022

Abstract
Background
Phlebotomine sand flies are vectors of Leishmania parasites, which are the causative agents of leishmaniasis. Herein, we developed an amplicon-based next-generation sequencing (Amp-NGS) to characterize sand flies and Leishmania parasites simultaneously targeting partial fragments of 18S rDNA and ITS1 genes, respectively.

Methods
Our assay was optimized using reference sand fly (n = 8) and Leishmania spp. (n = 9) samples and validated using wild-caught sand flies from Palestine. The assay was highly specific, and all DNA references were successfully identified to the species level.

Results
Among the wild-caught sand flies (n = 187), Phlebotomus spp. represented 95% of the collected samples (177/187), including Ph. sergenti (147/187, 79%), Ph. papatasi (19/187, 10.2%), Ph. perfiliewi (3/187, 1.6%), Ph. tobbi (2/187, 1.2%) and Ph. syriacus (6/187, 3.2%). Sergentomyia spp. represented only 5% (10/187) of the collected samples and included S. dentata (n = 6), S. fallax (n = 2), S. schwetzi (n = 1) and S. ghesquiere (n = 1). The study observed strong positive correlation between sand fly identification results of the Amp-NGS and morphological identification method (r = 0.84, df = 185, P < 0.001). Some discrepancies between the two methods in the identification of closely related species (i.e. Ph. perfiliewi, Ph. tobbi and Ph. syriacus) were observed. Leishmania DNA was detected and identified as L. tropica in 14 samples (14/187, 7.5%).

Conclusions
Our assay was sensitive to detect (limit of detection was 0.0016 ng/reaction) and identify Leishmania DNA in sand flies, thus representing a new tool for studying sand flies and their associated Leishmania parasites in endemic areas.

Graphical Abstract
Intensive care unit versus high-dependency care unit admission on mortality in patients with septic shock: a retrospective cohort study using Japanese claims data
Authors: Endo Koji , Mizuno Kayoko , Seki Tomotsugu , Joo Woo Jin , Takeda Chikashi , Takeuchi Masato , Kawakami Koji 
Published: July 2022

Abstract
Background
Septic shock is a common and life-threatening condition that requires intensive care. Intensive care units (ICUs) in Japan are classified into ICUs and high-dependency care units (HDUs), depending on presence of full-time certified intensivists and the number of assigned nurses. Compared with other developed countries, there are fewer intensive care beds and certified intensivists in Japan; therefore, non-intensivists often treat patients with septic shock in HDUs. It is unknown where we should treat patients with septic shock because no studies have compared the clinical outcomes between ICU and HDU treatment. This study aimed to elucidate which units should admit patients with septic shock by comparing mortality data and resource use between ICU and HDU admissions.

Methods
In this retrospective cohort study, we used a nationwide Japanese administrative database to identify adult patients with septic shock who were admitted to ICUs or HDUs between January 2010 and February 2021. The patients were divided into two groups, based on admittance to ICU or HDU on the day of hospitalization. The primary outcome was 30-day all-cause mortality adjusted for covariates using Cox regression analyses; the secondary outcomes were the length of ICU or HDU stay and length of hospital stay.

Results
Of the 10,818 eligible hospitalizations for septic shock, 6584 were in the ICU group, and 4234 were in the HDU group. Cox regression analyses revealed that patients admitted to the ICUs had lower 30-day mortality (adjusted hazard ratio: 0.89; 95% confidence interval: 0.83–0.96; P = 0.005). Linear regression analyses showed no significant difference in hospital length of stay or ICU or HDU length of stay.

Conclusions
An association was observed between ICU admission and lower 30-day mortality in patients with septic shock. These findings could provide essential insights for building a more appropriate treatment system.
Gross tumor volume delineation in primary prostate cancer on 18F-PSMA-1007 PET/MRI and 68Ga-PSMA-11 PET/MRI
Authors: Zhang Yan-Nan , Lu Zhen-Guo , Wang Shuai-Dong , Lu Xin , Zhu Lei-Lei , Yang Xu , Fu Li-Ping , Zhao Jun , Wang Hai-Feng , Xiang Zuo-Lin 
Published: July 2022

Abstract
Background
We aimed to assess the clinical value of 18F-PSMA-1007 and 68Ga-PSMA-11 PET/MRI in the gross tumor volume (GTV) delineation of radiotherapy for prostate cancer (PCa).

Methods
Sixty-nine patients were retrospectively enrolled (57 in the 18F subgroup and 12 in the 68Ga subgroup). Three physicians delineated the GTV and tumor length by the visual method and threshold method with thresholds of 30%, 40%, 50%, and 60% SUVmax. The volume correlation and differences in GTVs were assessed. The dice similarity coefficient (DSC) was applied to estimate the spatial overlap between GTVs. For 51 patients undergoing radical prostatectomy, the tumor length (Lpath) of the maximum area was measured, and compared with the longest tumor length obtained based on the images (LMRI, LPET/MRI, LPET, LPET30%, LPET40%, LPET50%, LPET60%) to determine the best delineation method.

Results
In the 18F subgroup, (1) GTV-PET/MRI (p < 0.001) was significantly different from the reference GTV-MRI. DSC between them was > 0.7. (2) GTV-MRI (R2 = 0.462, p < 0.05) was the influencing factor of DSC. In the 68Ga subgroup, (1) GTV-PET/MRI (p < 0.05) was significantly different from the reference GTV-MRI. DSC between them was > 0.7. (2) There was a significant correlation between GTV-MRI (r = 0.580, p < 0.05) and DSC. The longest tumor length measured by PET/MRI was in good agreement with that measured by histopathological analysis in both subgroups.

Conclusion
It is feasible to visually delineate GTV on PSMA PET/MRI in PCa radiotherapy, and we emphasize the utility of PET/MRI fusion images in GTV delineation. In addition, the overlap degree was the highest between GTV-MRI and GTV-PET/MRI, and it increased with increasing volume.
Cure rate and associated factors for children 6–59 months with severe acute malnutrition under the out patient therapeutic care programme in the health centres of Kabale District in Southwestern Uganda: a cross sectional study
Authors: ssekajja Vincent , Wamani Henry , Kitutu Freddy Eric , Atukwase Abel 
Published: July 2022

Abstract
Background
Severe acute malnutrition (SAM) is one of the leading causes of morbidity and mortality among children below five years with sub-Saharan Africa being the most affected. In Kabale district, SAM affects 2.9% children under the age of five. Uganda government introduced Outpatient therapeutic care (OTC) programme in all health centre level III and IV of Kabale. However, there was limited information about the cure rate and its associated factors among children under the programme hence the cause for the study.

Methods
A retrospective cross-sectional study was carried out on records of children 6–59 months (n = 637), presenting with SAM on OTC programme in the health centres of Kabale between 2013 and 2015. Data on cure rate (outcome) and other independent factors were collected, cleaned in excel and then exported into STATA 12 for analysis. Univariate, bivariate and logistic regression analysis was run to generate frequencies and factors associated.

Results
The cure rate was 36.3% (n = 231 cases) with a median recovery time of 21 days. The default rate was 58.6% (n = 373 cases) while the non-response and death rate were 0.6% (n = 4) and 1.1% (n = 7) respectively. Source at admission (Adjusted Odds Ratio [AOR] = 0.1, 95% CI 0.0, 0.7, p = 0.012), Weight at admission (AOR = 0.5, 95% CI 0.0, 0.9, p = 0.014) and Number of visits to the program (AOR = 14.9, 95% CI 9.3, 24.2, p = 0.040) were positively associated with cure rate of SAM children on OTC programme in Kabale.

Conclusion
Overall the cure and default rate for children on OTC programme in Kabale were significantly higher than national and international standards making the findings quite alarming. However, the weight of the child at admission, the number of visits to the programme to receive services and the source where the child was coming from were very important determinants of cure rate. To improve the cure rates of SAM children in Kabale, there is need for policy makers and programme implementers to think about a community based management of severe acute malnutrition program approach.
Motor speed does not impact the drift rate: a computational HDDM approach to differentiate cognitive and motor speed
Authors: Sandry Joshua , Ricker Timothy J. 
Published: July 2022

AbstractThe drift diffusion model (DDM) is a widely applied computational model of decision making that allows differentiation between latent cognitive and residual processes. One main assumption of the DDM that has undergone little empirical testing is the level of independence between cognitive and motor responses. If true, widespread incorporation of DDM estimation into applied and clinical settings could ease assessment of whether response disruption occurs due to cognitive or motor slowing. Across two experiments, we manipulated response force (motor speed) and set size to evaluate whether drift rates are independent of motor slowing or if motor slowing impacts the drift rate parameter. The hierarchical Bayesian drift diffusion model was used to quantify parameter estimates of drift rate, boundary separation, and non-decision time. Model comparison revealed changes in set size impacted the drift rate while changes in response force did not impact the drift rate, validating independence between drift rates and motor speed. Convergent validity between parameter estimates and traditional assessments of processing speed and motor function were weak or absent. Widespread application, including neurocognitive assessment where confounded changes in cognitive and motor slowing are pervasive, may provide a more process-pure measurement of information processing speed, leading to advanced disease-symptom management.
Perception of direct gaze in a video-conference setting: the effects of position and size
Authors: Horstmann Gernot , Linke Linda 
Published: July 2022

AbstractA common problem in video conferences is gaze direction. In face-to-face communication, it is common that speaker and listener intermittently look at each other. In a video-conference setting, where multiple participants are on the screen, things are complicated and not necessarily optimal. If the listener feels looked at when the speaker looks into the camera, how tolerant is the listener for slight deviations? And does this depend on the position of the speaker’s tile on the screen, or the size of the tile? In a first experiment, participants from a student population judged whether they are looked at, while vertical gaze direction of the looker was varied. Furthermore, the position of the tile on the screen varied. The results showed that a slightly upward directed gaze was optimal for the direct gaze judgment, with a width of ± 4 degrees. Optimal gaze direction was somewhat higher for tiles at the bottom of the screen. A second experiment tested the effect of size on the perception of horizontal gaze directions. Size was found to increase the gaze cone. The paper concludes with some recommendations for a setup of video conference systems, optimized for perceived gaze contact.
Hypertonic saline in ICU setting: what is its position? A systematic review and empirical analysis
Authors: Dornelles Marco , Dornelles Erik P. , Dornelles Larissa P. 
Published: July 2022

Abstract
Background
Fluid overload has been linked to poor outcomes in the critically ill in recent years, with multiple studies showing an increase in mortality in the overall intensive care unit population. Although the administration of hypertonic saline has increased in recent years, few publications involving its use in intensive care unit have been published to date. The aim of this systematic review is to compare hypertonic and isotonic saline solutions and assess the current evidence to determine whether hypertonic saline can be used in the intensive care unit to treat critically ill or injured patients.

Main body
The PRISMA protocol was applied to conduct the search, which generated 622 possible trials. Only four papers were chosen and included in our study after duplicates and studies that did not fulfill our inclusion criteria, and outcomes were removed. The primary outcome was mortality, with the length of time spent in intensive care and in the hospital as secondary outcomes, and patients assessed in the intensive care unit ranged from 3 to 55, according to our revision. There were three to 24 trials in all, and not all of them used mortality or intensive care unit stay as an endpoint. The concentration of HS used in the intervention group ranged from 1.4 to 30%, while not all studies used isotonic saline solution as a control group.

Conclusions
Despite the limited scientific evidence, there seems to be support for the administration/use of hypertonic saline in the intensive care unit setting, in highly selected circumstance. Although hypertonic saline may have favorable therapeutic effects, no effect on mortality has been demonstrated. Patients suffering from a traumatic brain injury evidence suggests that hypertonic saline can effectively lower intracranial pressure, and there is a new trend supporting the use of hypertonic sodium solutions in these situations. Our updated review shows that studies still have a lot of variability, and that more controlled research are needed.
Laccase-functionalized magnetic framework composite enabled chlorophenols degradation, a potential remediation for fungicides residues in leather
Authors: Cao Min , Yu Jie , Zhang Xing , Lin Yamei , Huang He 
Published: July 2022

Abstract
Chlorophenols, used as the fungicides in leather, are strictly limited in leather products. In this work, a metal–organic framework material, zeolitic metal azolate framework-7 (MAF-7), was first used to encapsulate laccase (Lac) to prepare MAF-7/Lac bio-composites with 98.5% immobilization yield. Afterward, Lac/MNP@MOM was formed by introducing the magnetic nanoparticles (MNPs) into the Lac@MOM. MAF-7 with better hydrophilicity and stronger pH buffering ability, exhibits good compatibility with laccase, which can reserve the activity of laccase after immobilization. Moreover, the porous structure of MAF-7 is favorable for the sufficient contact between laccase and substrates. Lac/MNP@MOM exhibited excellent activity when exposed to high temperature, extreme pH, and organic solvents, which also simplified complex recovery steps. Furthermore, the degradation rate of 2,4-dichlorophenol (2,4-DCP) could reach as high as 97% within 24 h by immobilized laccase, and after nine consecutive cycles of operation, enzyme activity could remain over 80%, which gives it the potential for practical applications.

Graphical abstract
Role of PET/CT in the follow-up of postoperative and/or post-therapy cancer rectum: comparison with pelvic MRI
Authors: Faheem Mohamed H. , Nathan Evram , Youssef Ahmed Farid 
Published: July 2022

Abstract
Background
In locally advanced rectal cancer, many imaging modalities are used, for example 18F-2-fluoro-2-deoxy-d-glucose (18F-FDG) positron emission tomography-computed tomography (PET-CT) and MRI. The aim of our study is to compare the diagnostic accuracy of 18 F-FDG-PET/CT & pelvic MRI; as well as to investigate the possible added value of using combined pelvic MRI and PET-CT for assessment of tumor response.

Results
Regarding the presence of local tumor, both PET CT and MRI showed perfect agreement with 97.1% overall accuracy, while in N category, PET CT showed higher specificity but lower sensitivity than MRI. MRI was superior to PET/CT in detecting extension to nearby organs; owing to the more anatomical details of MRI regarding the involvement of mesorectal fascia and EMVI. Almost total agreement of both MRI and PET/CT was noticed in evaluating post-therapy and postoperative complications.

Conclusion
For locally advanced rectal cancer (pT3–4 N0 M0 or any T N1 M0), a multimodality strategy has been shown to be the best option to evaluate local disease process, using the diagnostic criteria that were based on morphology, as well as glucose uptake, instead of the SUV alone for reassessment of post-therapy or postoperative changes.