bluuebunny/crossref_metadata_2025_split huggingface dataset:
ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data
Authors: Severin Jessica , Agrawal Saumya , Ramilowski Jordan A , Deviatiiarov Ruslan , Shin Jay W , Carninci Piero , de Hoon Michiel 
Published: August 2023

Abstract
In the genomic era, data dissemination and visualization is an integral part of scientific publications and research projects involving international consortia producing massive genome-wide data sets, intra-organizational collaborations, or individual labs. However, creating custom supporting websites is oftentimes impractical due to the required programming effort, web server infrastructure, and data storage facilities, as well as the long-term maintenance burden. ZENBU-Reports (https://fantom.gsc.riken.jp/zenbu/reports) is a web application to create interactive scientific web portals by using graphical interfaces while providing storage and secured collaborative sharing for data uploaded by users. ZENBU-Reports provides the scientific visualization elements commonly used in supplementary websites, publications and presentations, presenting a complete solution for the interactive display and dissemination of data and analysis results during the full lifespan of a scientific project both during the active research phase and after publication of the results.
Machine learning based lineage tree reconstruction improved with knowledge of higher level relationships between cells and genomic barcodes
Authors: Prusokiene Alisa , Prusokas Augustinas , Retkute Renata 
Published: August 2023

AbstractTracking cells as they divide and progress through differentiation is a fundamental step in understanding many biological processes, such as the development of organisms and progression of diseases. In this study, we investigate a machine learning approach to reconstruct lineage trees in experimental systems based on mutating synthetic genomic barcodes. We refine previously proposed methodology by embedding information of higher level relationships between cells and single-cell barcode values into a feature space. We test performance of the algorithm on shallow trees (up to 100 cells) and deep trees (up to 10 000 cells). Our proposed algorithm can improve tree reconstruction accuracy in comparison to reconstructions based on a maximum parsimony method, but this comes at a higher computational time requirement.
Combined inhibition of topoisomerase I and poly(ADP-ribose) polymerase: A synergistic therapeutic strategy for glioblastoma with phosphatase and tensin homolog deficiency
Authors: Kim Olga , Butler Madison , Sergi Zach , Robey Robert W , Zhang Meili , Chari Raj , Pang Ying , Yu Guangyang , Zhang Wei , Song Hua , Davis Dionne , Hawley Robert G , Wen Xinyu , Wang Herui , Quezado Martha , Tran Bao , Merchant Mythili , Ranjan Alice , Furnari Frank B , Khan Javed , Gilbert Mark R , Ryan Miller Christopher , Gottesman Michael M , Pommier Yves , Wu Jing 
Published: August 2023

Abstract

Background
Deletions or loss-of-function mutations in phosphatase and tensin homolog (PTEN) are common in glioblastoma (GBM) and have been associated with defective DNA damage repair. Here we investigated whether PTEN deficiency presents a vulnerability to a simultaneous induction of DNA damage and suppression of repair mechanisms by combining topoisomerase I (TOP1) and PARP inhibitors.

Methods
Patient-derived GBM cells and isogenic PTEN-null and PTEN-WT glioma cells were treated with LMP400 (Indotecan), a novel non-camptothecin TOP1 inhibitor alone and in combination with a PARP inhibitor, Olaparib or Niraparib. RNAseq analysis was performed to identify treatment-induced dysregulated pathways.

Results
We found that GBM cells lacking PTEN expression are highly sensitive to LMP400; however, rescue of the PTEN expression reduces sensitivity to the treatment. Combining LMP400 with Niraparib leads to synergistic cytotoxicity by inducing G2/M arrest, DNA damage, suppression of homologous recombination-related proteins, and activation of caspase 3/7 activity significantly more in PTEN-null cells compared to PTEN-WT cells. LMP400 and Niraparib are not affected by ABCB1 and ABCG2, the major ATP-Binding Cassette (ABC) drug efflux transporters expressed at the blood-brain barrier (BBB), thus suggesting BBB penetration which is a prerequisite for potential brain tumor treatment. Animal studies confirmed both an anti-glioma effect and sufficient BBB penetration to prolong survival of mice treated with the drug combination.

Conclusions
Our findings provide a proof of concept for the combined treatment with LMP400 and Niraparib in a subset of GBM patients with PTEN deficiency.
Ancrene Wisse
Authors: Milne Krista A. 
Published: August 2023

Judging from the significant number of copies that have survived, Ancrene Wisse (c. 1220–1230) was one of the most popular English works of the thirteenth century. The work was designed as a guide for religious recluses known as anchorites. Since it stands as an early example of Middle English from the West Midlands, Ancrene Wisse was of interest to early-20th-century philologists, including J. R. R. Tolkien. The work has attracted much attention as an early example of vernacular pastoralia—works designed to guide members of the Church through their religious lives. As one of the earliest surviving works of English literature addressed to women, Ancrene Wisse has also been the subject of feminist literary and historical analysis. As this brief survey suggests, the scholarship on Ancrene Wisse is vast, and this guide is intended to highlight some of the most influential and recent scholarship on the work.
Antibacterial Utilization for Febrile Illnesses and Laboratory-Confirmed Bloodstream Infections in Northern Tanzania
Authors: Moorthy Ganga S , Madut Deng B , Kilonzo Kajiru G , Lwezaula Bingileki F , Mbwasi Ronald , Mmbaga Blandina T , Ngocho James S , Saganda Wilbrod , Bonnewell John P , Carugati Manuela , Egger Joseph R , Hertz Julian T , Tillekeratne L Gayani , Maze Michael J , Maro Venance P , Crump John A , Rubach Matthew P 
Published: August 2023

Abstract

Background
We describe antibacterial use in light of microbiology data and treatment guidelines for common febrile syndromes in Moshi, Tanzania.

Methods
We compared data from 2 hospital-based prospective cohort studies, cohort 1 (2011–2014) and cohort 2 (2016–2019), that enrolled febrile children and adults. A study team member administered a standardized questionnaire, performed a physical examination, and collected blood cultures. Participants with bloodstream infection (BSI) were categorized as receiving effective or ineffective therapy based upon antimicrobial susceptibility interpretations. Antibacterials prescribed for treatment of pneumonia, urinary tract infection (UTI), or presumed sepsis were compared with World Health Organization and Tanzania Standard Treatment Guidelines. We used descriptive statistics and logistic regression to describe antibacterial use.

Results
Among participants, 430 of 1043 (41.2%) and 501 of 1132 (44.3%) reported antibacterial use prior to admission in cohorts 1 and 2, respectively. During admission, 930 of 1043 (89.2%) received antibacterials in cohort 1 and 1060 of 1132 (93.6%) in cohort 2. Inpatient use of ceftriaxone, metronidazole, and ampicillin increased between cohorts (P ≤ .002 for each). BSI was detected in 38 (3.6%) participants in cohort 1 and 47 (4.2%) in cohort 2. Of 85 participants with BSI, 81 (95.3%) had complete data and 52 (64.2%) were prescribed effective antibacterials. Guideline-consistent therapy in cohort 1 and cohort 2 was as follows: pneumonia, 87.4% and 56.8%; UTI, 87.6% and 69.0%; sepsis, 84.4% and 61.2% (P ≤ .001 for each).

Conclusions
Receipt of antibacterials for febrile illness was common. While guideline-consistent prescribing increased over time, more than one-third of participants with BSI received ineffective antibacterials.
Sprayed PAA-CaO2 nanoparticles combined with calcium ions and reactive oxygen species for antibacterial and wound healing
Authors: Yu Hong , Sun Jiale , She Kepeng , Lv Mingqi , Zhang Yiqiao , Xiao Yawen , Liu Yangkun , Han Changhao , Xu Xinyue , Yang Shuqing , Wang Guixue , Zang Guangchao 
Published: August 2023

Abstract
The most common socioeconomic healthcare issues in clinical are burns, surgical incisions and other skin injuries. Skin lesion healing can be achieved with nanomedicines and other drug application techniques. This study developed a nano-spray based on cross-linked amorphous calcium peroxide (CaO2) nanoparticles of polyacrylic acid (PAA) for treating skin wounds (PAA-CaO2 nanoparticles). CaO2 serves as a ‘drug’ precursor, steadily and continuously releasing calcium ions (Ca2+) and hydrogen peroxide (H2O2) under mildly acidic conditions, while PAA-CaO2 nanoparticles exhibited good spray behavior in aqueous form. Tests demonstrated that PAA-CaO2 nanoparticles exhibited low cytotoxicity and allowed L929 cells proliferation and migration in vitro. The effectiveness of PAA-CaO2 nanoparticles in promoting wound healing and inhibiting bacterial growth in vivo was assessed in SD rats using full-thickness skin defect and Staphylococcus aureus (S.aureus)-infected wound models based thereon. The results revealed that PAA-CaO2 nanoparticles demonstrated significant advantages in both aspects. Notably, the infected rats’ skin defects healed in 12 days. The benefits are linked to the functional role of Ca2+ coalesces with H2O2 as known antibacterial and healing-promoted agents. Therefore, we developed nanoscale PAA-CaO2 sprays to prevent bacterial development and heal skin lesions.
In vitro evaluation of microencapsulated organic acids and pure botanicals as a supplement in lactating dairy cows diet on in vitro ruminal fermentation
Authors: Lobo Richard R , Watson Michael , Vinyard James R , Johnson Mikayla L , Bahmam Aneesa , Ma Szu-Wei , Dagaew Gamonmas , Sumadong Phussorn , Sarmikasoglou Efstathios , Grilli Ester , Arce-Cordero Jose A , Faciola Antonio P 
Published: August 2023

Abstract
The utilization of microencapsulated organic acids and pure botanicals (mOAPB) is widely used in the monogastric livestock industry as an alternative to antibiotics; in addition, it can have gut immunomodulatory functions. More recently, an interest in applying those compounds in the ruminant industry has increased; thus, we evaluated the effects of mOAPB on ruminal fermentation kinetics and metabolite production in an in vitro dual-flow continuous-culture system. For this study, two ruminal cannulated lactating dairy Holstein cows were used as ruminal content donors, and the inoculum was incubated in eight fermenters arranged in a 4 × 4 Latin square design. The basal diet was formulated to meet the nutritional requirements of a 680-kg Holstein dairy cow producing 45 kg/d of milk and supplemented with increasing levels of mOAPB (0; 0.12; 0.24; or 0.36% of dry matter [DM]), which contained 55.6% hydrogenated and refined palm oil, 25% citric acid, 16.7% sorbic acid, 1.7% thymol, and 1% vanillin. Diet had 16.1 CP, 30.9 neutral detergent fiber (NDF), and 32.0 starch, % of DM basis, and fermenters were fed 106 g/d split into two feedings. After a 7 d adaptation, samples were collected for 3 d in each period. Samples of the ruminal content from the fermenters were collected at 0, 1, 2, 4, 6, and 8 h postmorning feeding for evaluation of the ruminal fermentation kinetics. For the evaluation of the daily production of total metabolites and for the evaluation of nutrient degradability, samples from the effluent containers were collected daily at days 8 to 10. The statistical analysis was conducted using MIXED procedure of SAS and treatment, time, and its interactions were considered as fixed effects and day, Latin square, and fermenter as random effects. To depict the treatment effects, orthogonal contrasts were used (linear and quadratic). The supplementation of mOAPB had no major effects on the ruminal fermentation, metabolite production, and degradability of nutrients. The lack of statistical differences between control and supplemented fermenters indicates effective ruminal protection and minor ruminal effects of the active compounds. This could be attributed to the range of daily variation of pH, which ranged from 5.98 to 6.45. The pH can play a major role in the solubilization of lipid coat. It can be concluded that mOAPB did not affect the ruminal fermentation, metabolite production, and degradability of dietary nutrients using an in vitro rumen simulator.
One genus, four different stories: evolutionary history, bionomics and biogeography of the monotypic tribe Stenostomatini (Coleoptera: Oedemeridae)
Authors: Poloni Riccardo , Bologna Marco A , Riccieri Alessandra 
Published: August 2023

Abstract
The false blister beetle tribe Stenostomatini includes only the genus Stenostoma, with four species showing an intriguing distribution: Stenostoma lowei (Madeira), Stenostoma cossyrense (Pantelleria), Stenostoma melitense (Malta and southern Sicily) and Stenostoma rostratum, widely distributed along the Mediterranean and North Atlantic coasts. The evolutionary history leading to this distribution has not been investigated. Here, we explore the phylogeny and evolutionary history of the tribe, adopting an integrative approach that combines morphological and molecular data (mitochondrial COI and nuclear CAD and 28S). Moreover, we propose a new key for species identification and update the knowledge on adult and larval ecology. Finally, we propose the following explanation for the current distribution of the species. The genus originated in the Miocene, with S. lowei belonging to the oldest lineage. The remaining species share a common ancestor, dating to the Messinian Salinity Crisis. Stenostoma melitense and S. cossyrense are well differentiated according to morphology, but not according to molecular analysis. The wide distribution of S. rostratum might be related to its strategy of laying eggs within beached driftwood, where larvae develop, easily transported by the currents. Given that neither morphological nor molecular differentiation was detected between the two subspecies of S. rostratum, we propose the new synonymy Stenostoma rostratum septentrionaleŠvihla, 2005 = Stenostoma rostratum (Fabricius, 1787) syn. nov.
Meta-analysis Investigating the Efficacy of Liquid Dressing and Ostomy Powder for the Treatment of Incontinence-Associated Dermatitis
Authors: Wang Jie , Ma Liang , Zhou Dan , Yu Bin-Hong 
Published: August 2023

ABSTRACT

OBJECTIVE
To study the effect of liquid dressing and ostomy powder on the treatment of incontinence-associated dermatitis (IAD).

METHODS
The authors searched PubMed, Web of Science, CNKI (China National Knowledge Internet), and Google Scholar databases for literature through July 28, 2022. After literature screening, two investigators independently extracted data from the included studies and applied the Newcastle-Ottawa Scale to assess the quality of the included studies. The χ
2-based Q statistic test and the I
2 statistic were used to measure the heterogeneity of the included studies. Publication bias was measured with funnel plots and the Egger test. Sensitivity analysis was conducted by eliminating each study one by one.

RESULTS
Four high-quality studies were included in the meta-analysis, involving a total of 307 participants. The meta-analysis results showed that compared with traditional care, treatment with liquid dressing and ostomy powder significantly improved the effective rate (pooled odds ratio, 21.42; 95% CI, 8.58 to 53.44), shortened the healing time (pooled mean difference, −10.73; 95% CI, −12.92 to −8.54), and reduced the recurrence rate (pooled mean difference, −2.03; 95% CI, −2.30 to −1.77) of IAD. Among the included studies, no publication bias was detected. Sensitivity analysis results confirmed the robustness of the pooled estimates.

CONCLUSIONS
Treatment with liquid dressing and ostomy powder has clinical value for patients with IAD.
A Systematic Review of Pressure Injuries Associated with Urethrocutaneous Fistula
Authors: Zogheib Serge , Khalil Nour , Mjaess Georges , Feghaly Charbel , Daou Bechara , Hanna Cyril , Nasr Marwan 
Published: August 2023

ABSTRACT

OBJECTIVE
To review the literature about combined urologic and reconstructive management of pressure injuries (PIs) with urethral fistulas.

DATA SOURCES
Authors searched the PubMed, MEDLINE, EMBASE, and Cochrane databases using the following keywords: “Perineum” or “Perineal” and “Pressure Ulcers” or ‘’ Pressure Injury‘’ and “Urethral Fistula.”

STUDY SELECTION
The search yielded a total of 95 articles. Study selection followed the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) statement, and the study was designed according to the PICOS (Population, Intervention, Comparison, Outcomes, Study) guidelines. Congress abstracts, letters to the editor, and editorial comments were excluded. After screening, a total of 9 studies (30 patients) were included in the review.

DATA EXTRACTION
Included patients received treatment for a perineal or ischial PI associated with a urinary fistula. The outcomes were recovery, complications, treatment failure, recurrence, and illness-related death.

DATA SYNTHESIS
Pressure injuries were mainly ischiatic (50%) and perineal (43%). Forty-six percent of patients had spinal cord injuries, and at least 40% reported voiding dysfunction. Sixteen percent had previous ischiectomy. Flaps such as posterior thigh flap, biceps femoris flap, and inferiorly based transverse rectus abdominal muscle flap had 88% to 100% success rates when used with urinary diversion techniques. Suprapubic cystostomy, the simplest method of urinary diversion, was successful in 47% of cases when performed alone and in 100% when combined with a pedicled omental flap or a transverse rectus abdominal muscle flap.

CONCLUSIONS
Prevention and wound care are essential for PI management, but when combined with a urinary fistula, surgical management is unavoidable. Urinary diversion is essential before undergoing any type of ulcer reconstruction. Urethral reconstruction showed favorable results, further strengthened when combined with a musculocutaneous flap.
The 2022 Update on Pressure Injuries: A Review of the Literature
Authors: Berlowitz Dan , Forget Julia G. , Saindon Kelley 
Published: August 2023

ABSTRACT
The pressure injury literature is rapidly growing, challenging busy clinicians who are trying to stay current. In this article, the authors summarize six articles published in 2022 that provide important new data or change how we may think about pressure injuries. The articles cover a range of topics including epidemiology, prevention, prediction, and nurse staffing. For each article, the authors provide a description of the study results along with a comment on why the results are important. This information will help clinicians remain current with the field and highlight new findings to incorporate into their clinical practice.

GENERAL PURPOSE
To review six articles published in 2022 that provide important new data or change how clinicians may think about pressure injuries.

TARGET AUDIENCE
This continuing education activity is intended for physicians, physician assistants, nurse practitioners, and nurses with an interest in skin and wound care.

LEARNING OBJECTIVES/OUTCOMES
After participating in this educational activity, the participant will:
1. Identify evidence-based risk factors for the development of pressure injuries (PIs).
2. Distinguish the predictors for PI development that prompted intervention.
3. Identify inconsistencies in documented stages of PIs.
4. Explain the impact of staffing on PI development rates.
Feasibility Assessment of a Biomarker-Guided Kidney-Sparing Sepsis Bundle: The Limiting Acute Kidney Injury Progression In Sepsis Trial
Authors: Gómez Hernando , Zarbock Alexander , Pastores Stephen M. , Frendl Gyorgy , Bercker Sven , Asfar Pierre , Conrad Steven A. , Creteur Jaques , Miner James , Mira Jean Paul , Motsch Johan , Quenot Jean-Pierre , Rimmelé Thomas , Rosenberger Peter , Vinsonneau Christophe , Birch Bob , Heskia Fabienne , Textoris Julien , Molinari Luca , Guzzi Louis M. , Ronco Claudio , Kellum John A. 
Published: August 2023

OBJECTIVES:
To determine the feasibility, safety, and efficacy of a biomarker-guided implementation of a kidney-sparing sepsis bundle (KSSB) of care in comparison with standard of care (SOC) on clinical outcomes in patients with sepsis.

DESIGN:
Adaptive, multicenter, randomized clinical trial.

SETTING:
Five University Hospitals in Europe and North America.

PATIENTS:
Adult patients, admitted to the ICU with an indwelling urinary catheter and diagnosis of sepsis or septic shock, without acute kidney injury (acute kidney injury) stage 2 or 3 or chronic kidney disease.

INTERVENTIONS:
A three-level KSSB based on Kidney Disease: Improving Global Outcomes (KDIGOs) recommendations guided by serial measurements of urinary tissue inhibitor of metalloproteinases-2 and insulin-like growth factor-binding protein 7 used as a combined biomarker [TIMP2]•[IGFBP7].

MEASUREMENTS AND MAIN RESULTS:
The trial was stopped for low enrollment related to the COVID-19 pandemic. Nineteen patients enrolled in five sites over 12 months were randomized to the SOC (n = 8, 42.0%) or intervention (n = 11, 58.0%). The primary outcome was feasibility, and key secondary outcomes were safety and efficacy. Adherence to protocol in patients assigned to the first two levels of KSSB was 15 of 19 (81.8%) and 19 of 19 (100%) but was 1 of 4 (25%) for level 3 KSSB. Serious adverse events were more frequent in the intervention arm (4/11, 36.4%) than in the control arm (1/8, 12.5%), but none were related to study interventions. The secondary efficacy outcome was a composite of death, dialysis, or progression of greater than or equal to 2 stages of acute kidney injury within 72 hours after enrollment and was reached by 3 of 8 (37.5%) patients in the control arm, and 0 of 11 (0%) patients in the intervention arm. In the control arm, two patients experienced progression of acute kidney injury, and one patient died.

CONCLUSIONS:
Although the COVID-19 pandemic impeded recruitment, the actual implementation of a therapeutic strategy that deploys a KDIGO-based KSSB of care guided by risk stratification using urinary [TIMP2]•[IGFBP7] seems feasible and appears to be safe in patients with sepsis.