bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of antimicrobial resistance and its clinical implications in Ethiopia: a systematic review
Authors: Berhe Derbew Fikadu , Beyene Getachew Tesfaye , Seyoum Berhanu , Gebre Meseret , Haile Kassa , Tsegaye Mulugeta , Boltena Minyahil Tadesse , Tesema Emawayish , Kibret Taddele Cherinet , Biru Mulatu , Siraj Dawd S. , Shirley Daniel , Howe Rawleigh , Abdissa Alemseged 
Published: December 2021

Abstract
Background
Antimicrobial resistance is one of the major public health challenges in Ethiopia. However, there is no comprehensive summary of existing AMR data in the country.

Aim
To determine the prevalence of antimicrobial resistance and its clinical implications in Ethiopia.

Methods
A systematic literature search was performed on the PubMed/Medline database. Original studies on antimicrobial resistance conducted in Ethiopia between 1st January 2009 and 31st July 2019 were included. The outcome measure was the number of isolates resistant to antimicrobial agents in terms of specific pathogens, and disease condition. Data was calculated as total number of resistant isolates relative to the total number of isolates per specific pathogen and medication.

Results
A total of 48,021 study participants enrolled from 131 original studies were included resulting in 15,845 isolates tested for antimicrobial resistance. The most common clinical sample sources were urine (28%), ear, nose, and throat discharge collectively (27%), and blood (21%). All the studies were cross-sectional and 83% were conducted in hospital settings. Among Gram-positive bacteria, the reported level of resistance to vancomycin ranged from 8% (Enterococcus species) to 20% (S. aureus). E. coli, K. pneumoniae and P. aeruginosa were the most common Gram-negative pathogens resistant to key antimicrobial agents described in the national standard treatment guideline and were associated with diverse clinical conditions: urinary tract infections, diarrhea, surgical site infections, pneumonia, ocular infections, and middle ear infections.

Conclusion
Overall, there is a high prevalence of antimicrobial resistance in Ethiopia. Empirical treatment of bacterial infections needs to be guided by up-to-date national guidelines considering local antimicrobial susceptibility patterns. Equipping diagnostic laboratories with culture and drug susceptibility testing facilities, and establishing a strong antimicrobial stewardship program should be high priorities.
Integrated enhanced Raman scattering: a review
Authors: Eslami Sahand , Palomba Stefano 
Published: December 2021

AbstractThe demand for effective, real-time environmental monitoring and for customized point-of-care (PoC) health, requires the ability to detect low molecular concentrations, using portable, reliable and cost-effective devices. However, traditional techniques often require time consuming, highly technical and laborious sample preparations, as well as expensive, slow and bulky instrumentation that needs to be supervised by laboratory technicians. Consequently, fast, compact, self-sufficient, reusable and cost-effective lab-on-a-chip (LOC) devices, which can perform all the required tasks and can then upload the data to portable devices, would revolutionize any mobile sensing application by bringing the testing device to the field or to the patient. Integrated enhanced Raman scattering devices are the most promising platform to accomplish this vision and to become the basic architecture for future universal molecular sensors and hence an artificial optical nose. Here we are reviewing the latest theoretical and experimental work along this direction.
Conquering the labour market: the socioeconomic enablement of refugee women in Austria
Authors: Schiestl David W. , Kittel Bernhard , Ibáñez Bollerhoff Maite 
Published: December 2021

AbstractRefugee women from the Near and Middle East face specific challenges when entering the Austrian labour market. Particularly gender-based factors, including care and reproductive work, exert pressure on these women and constitute major hurdles for successful entry into employment in Austria. Based on nine qualitative interviews with refugee women who swiftly gained entry to the labour market as well as ten qualitative interviews with experts from public and private support organisations, we investigate refugee women’s social and cultural capital as well as the individual agencies that foster paths into the labour market. We introduce the concept ofenablementas the process of gathering the preconditions for overcoming the challenges that arise on that path. Finally, we illuminate the ways in which the three dimensions of individual, relational and institutional enablement interrelate and shape individual agency with regard to labour market integration.
Inclusion of the fractured level into the construct of short segment fixation in patients with thoracolumbar fractures: clinical and radiological outcome
Authors: Hamdan Ali R. , Mahmoud Radwan Nouby , Tammam Ahmed G. , El-Khateeb Eslam El-Sayed 
Published: December 2021

AbstractBackgroundThoracolumbar fractures represent a widespread injuries that can cause significant disability and strain the healthcare system. Different surgical approaches are described in the literature. This study was conducted to evaluate the fractured level inclusion in short-segment fixation of thoracolumbar junction spine fractures.ResultsPreoperative neurological deficit was reported in seven patients ranging from ASIA grade C to D. All of these patients improved to grade E by the end of the follow-up period, except for one patient who improved from grade C to D. The mean Oswestry Disability Index was 19.87%. The mean postoperative Cobb angle was 11.77° which significantly improved compared to a preoperative value of 19.37°. There was a significant improvement in the postoperative anterior and posterior vertebral body height compared to the preoperative values. The vertebral body compression ratio significantly improved during the postoperative period to a mean of 84% compared to 76% preoperative.ConclusionsThere was significant improvement of the postoperative values of the mean Cobb angle, the anterior and the posterior vertebral body height as well as the vertebral body compression ratio compared to the preoperative values.
Prevalence of enterotoxin genes (SEA to SEE) and antibacterial resistant pattern of Staphylococcus aureus isolated from clinical specimens in Assiut city of Egypt
Authors: Baz Ahmed A. , Bakhiet Elsayed K. , Abdul-Raouf Usama , Abdelkhalek Ahmed 
Published: December 2021

Abstract
Background
Infections in communities and hospitals are mostly caused by Staphylococcus aureus strains. This study aimed to determine the prevalence of five genes (SEA, SEB, SEC, SED and SEE) encoding staphylococcal enterotoxins in S. aureus isolates from various clinical specimens, as well as to assess the relationship of these isolates with antibiotic susceptibility. Traditional PCR was used to detect enterotoxin genes, and the ability of isolates expressing these genes was determined using Q.RT-PCR.

Results
Overall; 61.3% (n = 46) of the samples were positive for S. aureus out of 75 clinical specimens, including urine, abscess, wounds, and nasal swabs. The prevalence of antibiotic resistance showed S. aureus isolates were resistant to Nalidixic acid, Ampicillin and Amoxicillin (100%), Cefuroxime (94%), Ceftriaxone (89%), Ciprofloxacin (87%), Erythromycin and Ceftaxime (85%), Cephalexin and Clarithromycin (83%), Cefaclor (81%), Gentamicin (74%), Ofloxacin (72%), Chloramphenicol(59%), Amoxicillin/Clavulanic acid (54%), while all isolates sensitive to Imipinem (100%). By employing specific PCR, about 39.1% of isolates were harbored enterotoxin genes, enterotoxin A was the most predominant toxin in 32.6% of isolates, enterotoxin B with 4.3% of isolates and enterotoxin A and B were detected jointly in 2.1% of isolates, while enterotoxin C, D and E weren’t detected in any isolate.

Conclusion
This study revealed a high prevalence of S. aureus among clinical specimens. The isolates were also multidrug resistant to several tested antibiotics. Enterotoxin A was the most prevalent gene among isolates. The presence of antibiotic resistance and enterotoxin genes may facilitate the spread of S. aureus strains and pose a potential threat to public health.
Impact of TP53 Genomic Alterations in Large B-Cell Lymphoma Treated With CD19-Chimeric Antigen Receptor T-Cell Therapy
Authors: Shouval Roni , Alarcon Tomas Ana , Fein Joshua A. , Flynn Jessica R. , Markovits Ettai , Mayer Shimrit , Olaide Afuye Aishat , Alperovich Anna , Anagnostou Theodora , Besser Michal J. , Batlevi Connie Lee , Dahi Parastoo B. , Devlin Sean M. , Fingrut Warren B. , Giralt Sergio A. , Lin Richard J. , Markel Gal , Salles Gilles , Sauter Craig S. , Scordo Michael , Shah Gunjan L. , Shah Nishi , Scherz-Shouval Ruth , van den Brink Marcel , Perales Miguel-Angel , Palomba Maria Lia 
Published: December 2021

PURPOSE Tumor-intrinsic features may render large B-cell lymphoma (LBCL) insensitive to CD19-directed chimeric antigen receptor T cells (CAR-T). We hypothesized that TP53 genomic alterations are detrimental to response outcomes in LBCL treated with CD19-CAR-T. MATERIALS AND METHODS Patients with LBCL treated with CD19-CAR-T were included. Targeted next-generation sequencing was performed on pre–CAR-T tumor samples in a subset of patients. Response and survival rates by histologic, cytogenetic, and molecular features were assessed. Within a cohort of newly diagnosed LBCL with genomic and transcriptomic profiling, we studied interactions between cellular pathways and TP53 status. RESULTS We included 153 adults with relapsed or refractory LBCL treated with CD19-CAR-T (axicabtagene ciloleucel [50%], tisagenlecleucel [32%], and lisocabtagene maraleucel [18%]). Outcomes echoed pivotal trials: complete response (CR) rate 54%, median overall survival (OS) 21.1 months (95% CI, 14.8 to not reached), and progression-free survival 6 months (3.4 to 9.7). Histologic and cytogenetic LBCL features were not predictive of CR. In a subset of 82 patients with next-generation sequencing profiling, CR and OS rates were comparable with the unsequenced cohort. TP53 alterations (mutations and/or copy number alterations) were common (37%) and associated with inferior CR and OS rates in univariable and multivariable regression models; the 1-year OS in TP53-altered LBCL was 44% (95% CI, 29 to 67) versus 76% (65 to 89) in wild-type ( P = .012). Transcriptomic profiling from a separate cohort of patients with newly diagnosed lymphoma (n = 562) demonstrated that TP53 alterations are associated with dysregulation of pathways related to CAR-T-cell cytotoxicity, including interferon and death receptor signaling pathway and reduced CD8 T-cell tumor infiltration. CONCLUSION TP53 is a potent tumor-intrinsic biomarker that can inform risk stratification and clinical trial design in patients with LBCL treated with CD19-CAR-T. The role of TP53 should be further validated in independent cohorts.
PDBrt: A free database of complexes with measured drug-target residence time
Authors: Ługowska Magdalena , Pacholczyk Marcin 
Published: December 2021

Background: Difficulties in translating the in vitro potency determined by cellular assays into in vivo efficacy in living organisms complicates the design and development of drugs. However, the residence time of a drug in its molecular target is becoming a key parameter in the design and optimization of new drugs, as recent studies show that residence time can reliably predict drug efficacy in vivo. Experimental approaches to binding kinetics and target ligand complex solutions are currently available, but known bioinformatics databases do not usually report information about the ligand residence time in its molecular target. Methods: To extend existing databases we developed the Protein Data Bank (PDB) residence time database (PDBrt) which reports drug residence time. The database is implemented as an open access web-based tool. The front end uses Bootstrap with Hypertext Markup Language (HTML), jQuery for the interface and 3Dmol.js to visualize the complexes. The server-side code uses Python web application framework, Django Rest Framework and backend database PostgreSQL. Results: The PDBrt database is a free, non-commercial repository for 3D protein-ligand complex data, including the measured ligand residence time inside the binding pocket of the specific biological macromolecules as deposited in The Protein Data Bank. The PDBrt database contains information about both the protein and the ligand separately, as well as the protein-ligand complex, binding kinetics, and time of the ligand residence inside the protein binding site. Availability: https://pdbrt.polsl.pl
10-year longitudinal study of malaria in children: Insights into acquisition and maintenance of naturally acquired immunity
Authors: Addy John W.G. , Bediako Yaw , Ndungu Francis M. , Valetta John Joseph , Reid Adam J. , Mwacharo Jedida , Ngoi Joyce Mwongeli , Wambua Joshua , Otieno Edward , Musyoki Jennifer , Said Khadija , Berriman Matthew , Marsh Kevin , Bejon Philip , Recker Mario , Langhorne Jean 
Published: December 2021

Background: Studies of long-term malaria cohorts have provided essential insights into how Plasmodium falciparum interacts with humans, and influences the development of antimalarial immunity. Immunity to malaria is acquired gradually after multiple infections, some of which present with clinical symptoms. However, there is considerable variation in the number of clinical episodes experienced by children of the same age within the same cohort. Understanding this variation in clinical symptoms and how it relates to the development of naturally acquired immunity is crucial in identifying how and when some children stop experiencing further malaria episodes. Where variability in clinical episodes may result from different rates of acquisition of immunity, or from variable exposure to the parasite. Methods: Using data from a longitudinal cohort of children residing in an area of moderate P. falciparum transmission in Kilifi district, Kenya, we fitted cumulative episode curves as monotonic-increasing splines, to 56 children under surveillance for malaria from the age of 5 to 15. Results: There was large variability in the accumulation of numbers of clinical malaria episodes experienced by the children, despite being of similar age and living in the same general location. One group of children from a particular sub-region of the cohort stopped accumulating clinical malaria episodes earlier than other children in the study. Despite lack of further clinical episodes of malaria, these children had higher asymptomatic parasite densities and higher antibody titres to a panel of P. falciparum blood-stage antigens. Conclusions: This suggests development of clinical immunity rather than lack of exposure to the parasite, and supports the view that this immunity to malaria disease is maintained by a greater exposure to P. falciparum, and thus higher parasite burdens. Our study illustrates the complexity of anti-malaria immunity and underscores the need for analyses which can sufficiently reflect the heterogeneity within endemic populations.
Drivers of menstrual material disposal and washing practices: A systematic review
Authors: Robinson Hannah Jayne , Barrington Dani Jennifer 
Published: December 2021

Background
Disposal and washing facilities and services for menstrual materials are often designed based upon technical specifications rather than an in-depth understanding of what drives peoples’ choices of practices.

Objectives and data sources
This systematic review identified and summarised the main behavioural drivers pertaining to the choice of disposal and washing practices of menstrual materials through the thematic content analysis and study appraisal of 82 publications (80 studies) on menstrual health and hygiene published since 1999, reporting the outcomes of primary research across 26 countries.

Results
Disposal and washing behaviours are primarily driven by the physical state of sanitation facilities; however, this is intrinsically linked to taboos surrounding and knowledge of menstruation.

Implications
Using reasons given for disposal and washing practices by menstruators or those who know them well, or inferred by authors of the reviewed studies, we identify the key considerations needed to design facilities and services which best suit the desired behaviours of both planners and those who menstruate.

Inclusivity
The term menstruators is used throughout to encompass all those mentioned in the studies reviewed (girls and women); although no studies explicitly stated including non-binary or transgender participants, this review uses inclusive language that represents the spectrum of genders that may experience menstruation.

Registration
The review protocol is registered on PROSPERO: 42019140029.
Analysis of case fatality rate of SARS-CoV-2 infection in the Spanish Autonomous Communities between March and May 2020
Authors: V. Martín-Sánchez , A. Calderón-Montero , A. Barquilla-García , F. Vitelli-Storelli , A. Segura-Fragoso , V. Olmo-Quintana , A. Serrano-Cumplido ,   on behalf of the COVID-19 Group of the Spanish Society of Primary Care Physicians (SEMERGEN)
Published: December 2021

Objective
The Spanish health system is made up of seventeen regional health systems. Through the official reporting systems, some inconsistencies and differences in case fatality rates between Autonomous Communities (CC.AA.) have been observed. Therefore the objective of this paper is to compare COVID-19 case fatality rates across the Spanish CC.AA.

Material and methods
Observational descriptive study. The COVID-19 case fatality rate (CFR) was estimated according to the official records (CFR-PCR+), the daily mortality monitory system (MoMo) record (CFR-Mo), and the seroprevalence study ENE-COVID-19 (Estudio Nacional de sero Epidemiologia Covid-19) according to sex, age group and CC.AA. between March and June 2020. The main objective is to detect whether there are any differences in CFR between Spanish Regions using two different register systems, i. e., the official register of the Ministry of Health and the MoMo.

Results
Overall, the CFR-Mo was higher than the CFR-PCR+, 1.59% vs 0.98%. The differences in case fatality rate between both methods were significantly higher in Castilla La Mancha, Castilla y León, Cataluña, and Madrid. The difference between both methods was higher in persons over 74 years of age (CFR-PCR+ 7.5% vs 13.0% for the CFR-Mo) but without statistical significance. There was no correlation of the estimated prevalence of infection with CFR-PCR+, but there was with CFR-Mo (R2 = 0.33). Andalucía presented a SCFR below 1 with both methods, and Asturias had a SCFR higher than 1. Cataluña and Castilla La Mancha presented a SCFR greater than 1 in any scenario of SARS-CoV-2 infection calculated with SCFR-Mo.

Conclusions
The PCR+ case fatality rate underestimates the case fatality rate of the SARS-CoV- 2 virus pandemic. It is therefore preferable to consider the MoMo case fatality rate. Significant differences have been observed in the information and registration systems and in the severity of the pandemic between the Spanish CC.AA. Although the infection prevalence correlates with case fatality rate, other factors such as age, comorbidities, and the policies adopted to address the pandemic can explain the differences observed between CC.AA.
Effect of changes in cerebral oximeter values during cardiac surgery on the incidence of postoperative neurocognitive deficits (POND): A retrospective study based on propensity score–matched analysis
Authors: Ahn Jin Hee , Lee Eun kyung , Kim Doyeon , Kang SeHee , Choi Won-Jun , Byun Jae-hun , Shim Jae-Geum , Lee Sung Hyun 
Published: December 2021

Objectives
The occurrence of postoperative neurocognitive deficits(POND)after major cardiac surgery is associated with an increase in perioperative mortality and morbidity. Oxidative stress caused by oxygen can affect neuronal damage, which can lead to POND. Whether the intraoperative rSO2 value reflects oxidative stress and the associated incidence of POND is unknown.

Methods
Among 3482 patients undergoing cardiac surgery, 976 patients were allocated for this retrospective study. Of these, 230 patients (32.5%) were observed to have postoperative neurologic symptoms. After propensity score 1:2 ratio matching, a total of 690 patients were included in the analysis. Recorded data on the occurrence of POND from the postoperative period to predischarge were collected from the electronic records.

Results
The mean baseline rSO2 value was higher in the POND (–) group than in the POND (+) group. The mean overall minimum rSO2 value was lower in the POND (+) group (52.2 ± 8.3 vs 48.3 ± 10.5, P < 0.001). The mean overall maximum rSO2 values were not significantly different between the two groups (72.7 ± 8.3 vs 73.2 ± 9.2, P = 0.526). However, there was a greater increase in the overall maximum rSO2 values as compared with baseline in the POND (+) group (10.9 ± 8.2 vs 17.9 ± 10.2, P < 0.001). The degree of increase in the maximum rSO2 value was a risk factor affecting the occurrence of POND (adjusted odds ratio, 1.08; 95% confidence interval [CI], 1.04–1.11; P < 0.001). The areas under the receiver-operating characteristic curve for delta values of minimal and maximal compared with baseline values were 0.60 and 0.71, respectively.

Conclusions
Increased cerebral oximeter levels during cardiac surgery may also be a risk factor for POND. This is considered to reflect the possibility of oxidative neuronal damage, and further studies are needed in the future.
Morse theory and the calculus of variations
Authors: Tromba Anthony 
Published: December 2021

Abstract
We prove for the first time that classical Morse theory applies to functionals of the form

𝒥
⁢

(
u
)

=

1
2

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∫
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A

α
⁢
β

i
⁢
j

⁢

(
x
)

⁢

∂
⁡

u
i

∂
⁡

x
α

⁢

∂
⁡

u
j

∂
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x
β

⁢

𝑑
x

+

∫
Ω

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(
x
,
u
)

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\displaystyle\mathcal{J}(u)=\frac{1}{2}\int_{\Omega}A^{ij}_{\alpha\beta}(x)%
\frac{\partial u^{i}}{\partial x^{\alpha}}\frac{\partial u^{j}}{\partial x^{%
\beta}}\,dx+\int_{\Omega}G(x,u)\,dx

where

u
:

Ω
→

ℝ
N

{u:\Omega\to\mathbb{R}^{N}}

,

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⊂

ℝ
n

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compact with

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∞

{C^{\infty}}

boundary

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{\partial\Omega}

,

u
|

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=
φ

{u|_{\partial\Omega}=\varphi}

, and we argue that this is the largest class to which Morse theory applies.
„ … unter allerlei Plunder eine alte zerfetzte Landkarte“ Papyrus P 11702: Anmerkungen zu den Zeichnungen
Authors: Vaelske Veit , Durot Nathalie , Gerhardt Marius 
Published: December 2021

Abstract
Analysis of the drawings on a 5th century AD papyrus containing a list of multiplications. On the recto, an eagle with XI monogram emblematises the Christian notion of resurrection and ascent of the soul. On the verso, what was earlier considered just an ornament is in fact a geographical map of an Eastern Desert wadi and is fashioned following patterns of older Egyptian cartography.
A strategos on Trial before the Provincial Governor: a New Look at a Petition to the Roman Prefect of Egypt (P.Wisc. I 33)
Authors: Dolganov Anna 
Published: December 2021

Abstract
P.Wisc. 1 33 is a petition reporting an act of violence, supposedly committed against a strategos of the Arsinoite nome. A re-examination of the papyrus reveals that the strategos in question was not the victim, but was himself being summoned for trial before the governor. The document thereby attests to the most high-profile prosecution of an official in Roman Egypt for which documentary evidence survives.