bluuebunny/crossref_metadata_2025_split huggingface dataset:
ADVISE: Accelerating the Creation of Evidence Syntheses for Global Development Using Natural Language Processing-Supported Human-Artificial Intelligence Collaboration
Authors: Edwards Kristen M. , Song Binyang , Porciello Jaron , Engelbert Mark , Huang Carolyn , Ahmed Faez 
Published: December 2023

Abstract
When designing evidence-based policies and programs, decision-makers must distill key information from a vast and rapidly growing literature base. Identifying relevant literature from raw search results is time and resource intensive, and is often done by manual screening. In this study, we develop an artificial intelligence (AI) agent based on a bidirectional encoder representations from transformers (BERT) model and incorporate it into a human team designing an evidence synthesis product for global development. We explore the effectiveness of the human–AI hybrid team in accelerating the evidence synthesis process. To further improve team efficiency, we enhance the human–AI hybrid team through active learning (AL). Specifically, we explore different sampling strategies, including random sampling, least confidence (LC) sampling, and highest priority (HP) sampling, to study their influence on the collaborative screening process. Results show that incorporating the BERT-based AI agent into the human team can reduce the human screening effort, i.e., the number of documents that humans need to screen, by 68.5% compared to the case of no AI assistance and by 16.8% compared to the industry-standard case of using a frequency-based language model and support vector machine-based classifier for identifying 80% of all relevant documents. When we apply the HP sampling strategy, the human screening effort can be reduced even more: by 78.3% for identifying 80% of all relevant documents compared to no AI assistance. We apply the AL-enhanced human–AI hybrid teaming workflow in the design process of three evidence gap maps for U.S. Agency for International Development and find it to be highly effective. These findings demonstrate how AI can accelerate the development of evidence synthesis products and promote timely evidence-based decision-making in global development.
Population pharmacokinetics and target attainment analysis of vancomycin after intermittent dosing in adults with cystic fibrosis
Authors: Yellepeddi Venkata K. , Lindley Bryn , Radetich Emi , Kumar Shaun , Bhakta Zubin , Leclair Laurie , Parrot Madison , Young David C. 
Published: December 2023

ABSTRACT

Vancomycin is the first-line agent to treat pulmonary infections caused by methicillin-resistant
Staphylococcus aureus
(MRSA) in people with cystic fibrosis (PwCF). However, there is no consensus on vancomycin initial dosing in this population among health institutions, and there is a large variability in initial dosing across the United States. In this study, we characterized the pharmacokinetics (PK) of vancomycin in PwCF using a population PK approach. The clinical PK data to develop the population PK model were obtained from vancomycin therapeutic monitoring data from PwCF undergoing treatment for infections due to MRSA. The population PK model was then used to perform comprehensive Monte Carlo simulations to evaluate the probability of target attainment (PTA) of 12 different initial dosing scenarios. The area under the curve to minimum inhibitory concentration (MIC) ratio ≥400 mg*h/L and <650 mg*h/L were used as efficacy and toxicity targets for PTA analysis. A total of 181 vancomycin plasma concentrations were included in the analysis. A one-compartment model with first-order elimination best described the data. Weight significantly influenced the vancomycin PK (
P
< 0.05). In the final model, clearance was estimated as 5.52 L/h/70 kg, and the volume of distribution was 31.5 L/70 kg. The PTA analysis showed that at MIC = 1 µg/mL, doses 1,500 q8h and 2,000 q12h showed the highest %PTA in achieving both efficacy and toxicity targets. The PTA results from this study may potentially inform the initial dosing regimens of vancomycin to treat pulmonary infections due to MRSA in PwCF.
Bacteriophage infection and killing of intracellular
Mycobacterium abscessus
Authors: Schmalstig Alan A. , Wiggins Andrew , Badillo Debbie , Wetzel Katherine S. , Hatfull Graham F. , Braunstein Miriam 
Published: December 2023

ABSTRACT

Mycobacterium abscessus
is a nontuberculous mycobacteria that contributes to the decline and death of patients with lung diseases such as cystic fibrosis and other muco-obstructive airway diseases.
M. abscessus
is challenging to treat due to its extensive antibiotic resistance and ability to survive inside mammalian cells. An alternative to antibiotics is the therapeutic use of bacteriophages (phages). There are recent cases of phage therapy being used to treat
M. abscessus
infections in people under compassionate-use conditions. However, little is known about the ability of phages to kill bacteria, such as
M. abscessus
, which reside in an intracellular environment. Here, we used
M. abscessus
strains and phages from recent phage therapy cases to determine if phages can enter mammalian cells and if they can infect and kill intracellular
M. abscessus
. Using fluorescence microscopy, we demonstrate phage uptake by macrophages and lung epithelial cells, and we further demonstrate phage infection of intracellular
M. abscessus
with fluorescent reporter phages. Transmission electron microscopy was additionally used to image phage infection of intracellular
M. abscessus
. Together, these findings provide the first visualizations of phage-
M. abscessus
interactions in an intracellular environment. Finally, we show that phage treatment can significantly reduce the intracellular burden of
M. abscessus
in a manner that depends on both the specific phage and mammalian cell type involved. These results demonstrate the potential to use phage therapy to treat intracellular bacteria, specifically
M. abscessus
, while also highlighting the importance of prescreening phage therapy candidates for activity in an intracellular environment.

IMPORTANCE

As we rapidly approach a post-antibiotic era, bacteriophage (phage) therapy may offer a solution for treating drug-resistant bacteria.
Mycobacterium abscessus
is an emerging, multidrug-resistant pathogen that causes disease in people with cystic fibrosis, chronic obstructive pulmonary disease, and other underlying lung diseases.
M. abscessus
can survive inside host cells, a niche that can limit access to antibiotics. As current treatment options for
M. abscessus
infections often fail, there is an urgent need for alternative therapies. Phage therapy is being used to treat
M. abscessus
infections as an option of last resort. However, little is known about the ability of phages to kill bacteria in the host environment and specifically in an intracellular environment. Here, we demonstrate the ability of phages to enter mammalian cells and to infect and kill intracellular
M. abscessus
. These findings support the use of phages to treat intracellular bacterial pathogens.
Integrated Re-Os, Ar/Ar, and U-Pb geochronology directly dates the timing of mineralization at the Mina Justa and Marcona deposits, Peru
Authors: Rodríguez-Mustafa María A. , Simon Adam C. , Holder Robert M. , Stein Holly , Kylander-Clark Andrew R.C. , Jicha Brian R. , Blakemore Daniel , Machado Edson L.B. 
Published: December 2023

Abstract
Iron oxide–copper–gold (IOCG) and iron oxide–apatite (IOA) deposits are important sources of Cu and Fe, respectively. They contain abundant Fe-oxides and may contain Au, Ag, Co, rare earth elements (REEs), U, Ni, and V as economically important by-products. In Peru, the Mina Justa IOCG deposit is located next to the giant Marcona IOA deposit. Constraining the timing of Fe and Cu mineralization at Mina Justa is fundamental to understanding the duration and type of processes that generated this mineral deposit, and ultimately to testing the genetic link with other deposits in the area. Previous authors used alteration minerals to indirectly date Cu mineralization at Mina Justa at around 100 Ma. We report Ar/Ar dates of actinolite, U-Pb dates of magnetite, apatite, and titanite collected by in situ laser-ablation–multicollector–inductively coupled plasma–mass spectrometry, and Re-Os thermal ionization mass spectrometry dates for sulfides. These results indicate that Cu mineralization at Mina Justa occurred at ca. 160 Ma and that Fe mineralization is older and coeval with the neighboring Marcona IOA deposit, consistent with Cu mineralization overprinting IOA-style mineralization at Mina Justa.
Multicentric evaluation of a specific intrathecal anti-Treponema pallidumIgG index as a diagnostic biomarker of neurosyphilis: results from a retro-prospective case–control study
Authors: Alberto Chloé , Lambeng Nathalie , Deffert Christine , Breville Gautier , Gayet-Ageron Angèle , Lalive Patrice , Calmy Alexandra , Coste Alix , Papadimitriou-Olivgeris Matthaios , Braun Dominique , Lienhard Reto , Bosshard Philipp Peter , Fontao Lionel , Toutous Trellu Laurence 
Published: December 2023

Background and objectivesThe diagnosis of neurosyphilis (NS) lacks a true ‘gold standard’, making the diagnosis challenging while consequences of a misdiagnosis are potentially severe. The aim of this study was to evaluate the diagnostic performance of measuring an antibody index (AI) for the intrathecal synthesis of specific anti-Treponema pallidum(T. pallidum) IgG for the diagnosis of NS.MethodsSpecific anti-T. pallidumIgG were measured simultaneously in paired cerebrospinal fluid (CSF)–serum samples collected retrospectively and prospectively between 2007 and 2022, from patients suspected of NS, in Switzerland. An AI was calculated to account for blood–brain barrier integrity. Area under the receiver operating characteristic curve, sensitivity/specificity and positive/negative predictive values of AI test were estimated. Two NS definitions were used: NS1 included patients with NS suspicion presenting with neurological symptoms and/or acute neurosensory signs, and positiveT. PallidumHemagglutinations Assay (TPHA)/T. pallidumparticle agglutination assay (TPPA) serology and CSF-TPHA/TPPA ≥320, and either CSF-leucocytes >5 cells/mm3and/or CSF-protein >0.45 g/L and/or a reactive CSF-venereal disease research laboratory (VDRL)/rapid plasma reagin (RPR) test. NS2 included patients with suspected NS presenting with acute ocular and/or otologic symptoms, and positive TPHA/TPPA serology, and a favourable response to NS treatment. Controls were patients diagnosed with any other central nervous system (CNS) pathologies and with positive TPHA/TPPA serology.ResultsThe study included 71 NS (43 NS1 and 28 NS2) and 110 controls. With a threshold of ≥1.7, sensitivity and specificity of the specific AI test were 90.7% (CI 77.7 to 97.4) and 100% (CI 96.7 to 100.0), respectively, for NS1 and 14.3% (CI 4 to 32.7) and 100% (CI 96.7 to 100.0) for NS2. In patients suspected of NS with a CNS involvement (NS1 group), NS could be confirmed by the positivity of this specific AI.ConclusionsMeasurement of an intrathecal synthesis index of specific anti-T. pallidumIgG in patients with CSF inflammatory signs appears to be a valuable diagnostic test. However, in otic or ocular syphilis, presenting few CSF abnormalities, AI is not sufficient alone to confirm NS diagnosis.Trial registrationSwiss Association of Research Ethics Committees number 2019-00232.
Intussusception reveals MUTYH-related polyposis syndrome and colorectal cancer
Authors: Nii Fernanda , Medeiros Kayo Augusto de Almeida , Carvalho Bárbara Justo , Martines Diego Ramos , Mesquita Gustavo Heluani Antunes de , Waisberg Daniel Reis , Meyer Alberto 
Published: December 2023

We are reporting a rare case of MUTYH-associated polyposis, a colorectal cancer hereditary syndrome, diagnosticated after an intussusception. Colorectal cancer is an important cause of cancer related mortality that can be manifested by an intussusception, a rare occurrence in adults and almost always related to tumors. Approximately 5% of colorectal cancers can be attributed to syndromes known to cause hereditary colorectal cancer, such as MUTYHassociated polyposis, autosomal genetic syndrome associated with this disease. We present the case of a 44 years old male, that sought medical consultation with a complaint of abdominal discomfort, that after five days changed its characteristics. The patient was sent to the emergency department were a CT-scan revealed intestinal sub-occlusion by ileocolic invagination. Right colectomy was carried out. The anatomic-pathological examination revealed a moderately differentiated mucinous adenocarcinoma and multiples sessile polyps, which led to the suspicion of a genetic syndrome. In the genetics analysis two mutations were observed in the MUTYH gene, and MUTYH-associated polyposis was diagnosticated. This case demonstrates the importance of meticulous analysis of the patient examinations results to identify possible discrete alterations that can lead to improved understanding of disease.
Rate of complications due to carotid angioplasty in a tertiary university hospital
Authors: Macêdo Isabella Sales de , Alquéres Rafaela Almeida , Schneider Lorena Souza Viana , Puglia Júnior Paulo , Conforto Adriana Bastos 
Published: December 2023

Introduction: Stenoses greater than 50% in the cervical internal carotid artery cause up to 8% of all ischemic strokes. Carotid artery stenting (CAS) is an effective alternative to prevent cerebrovascular events to occur. According to recommendations from the American Heart Association/American Stroke Association, CAS is indicated for symptomatic patients with internal carotid stenosis greater than 70% (measured by non-invasive methods), as long as the risk for periprocedural stroke or death is less than 6%. There is few information about complication rates of CAS in developing countries. Objectives: The primary goal of this study was to evaluate the frequency of any stroke or death until hospital discharge after CAS in symptomatic patients with carotid stenosis in a tertiary university hospital. Other complication rates were also assessed as secondary aims. Methods: A single-center retrospective study based on the analysis of charts from patients submitted to CAS between April 2011 and March 2016. Inclusion criteria were: age ≥ 18 years old, admission and follow-up by neurologists from the Neurology Ward, performance of CAS according to the hospital´s protocol (carotid stenosis ≥70%, patients with transient ischemic attack (TIA), amaurosis fugax or minor stroke in the last 180 days, and life expectancy greater than a year). Patients not followed by neurologists after CAS were excluded. Results: A total of 65 patients were included: 3 (4.6%) suffered stroke or death after CAS. Two of these patients presented ischemic strokes and one, an hemorrhagic stroke that lead to death. Myocardial infarctions were not identified, as well as carotid ruptures or dissections, hyperperfusion syndrome, artery perforations, stent thrombosis or encephalopathy. Minor complication rates were: 12.3% for hypotension, 9.2% for bradycardia, 1.5% for TIA, 3.1% for carotid vasospasm and 6.2% for acute kidney injury. The total rate of minor complications was 23.1%, and none of then led to permanent harm. Conclusions: The rate of stroke or death in a reference tertiary service in a developing country was in line with international recommendations.
Food consumption and cardiovascular risk in disease-free women with polycystic ovary syndrome: a cross-sectional study in Northeast Brazil
Authors: Moreira Leonardo Victor Galvão , Mendes Matheus Veras Guterres , Sousa Rosângela Maria Lopes de , Chein Maria Bethânia da Costa , Brito Luciane Maria Oliveira 
Published: December 2023

Objective: To investigate the association between dietary intake, nutritional status and cardiovascular risk markers in women with polycystic ovary syndrome (PCOS) without other chronic diseases.Methods: This cross-sectional study included 59 women diagnosed with PCOS and 126 age-matched healthy controls. Data collected consisted of socio-demographic and behavioral variables, weight, height, body mass index (BMI), waist circumference (WC), waist-to-height ratio (WHTR), lipid accumulation products (LAP), serum triglycerides (TG) level, body fat percentage (BFP), and food consumption. Quantitative and qualitative food intake were verified by applying a food frequency questionnaire.Results: BMI, WC, WHTR and LAP index values as well as TG levels, but not BFP values, were significantly increased in the PCOS group as compared to controls (p<0.05). In the control group, eutrophic women had slightly higher TG levels, whereas obese women were younger in the PCOS group (p<0.05). In both groups, the consumption of carbohydrates and proteins was adequate, but fiber intake was insufficient. In the PCOS group, energy consumption was excessive, while carbohydrate intake was higher than in controls, but adequate.Conclusion: Although diseasefree PCOS women showed enhanced inadequacy in dietary intake and nutritional status and increased cardiovascular impairment, no correlation between dietary intake, nutritional status and cardiovascular risk markers was found.Key words: Polycystic ovary syndrome; Eating; Cardiovascular diseases; Nutritional status.
effect of botulinum toxin type A injection in the viability of dorsal flap in rats
Authors: Medeiros Sofia Amaral , Camargo Cristina Pires , Gemperli Rolf 
Published: December 2023

Purpose: Botulinum toxin A (BoNTA) increased the viability of skin flap in healthy rats. Most of the studies injected this substance some days (7-15) before the flap surgery. This treatment is used only for elective surgery, there was no data about the efficacy of BontA when injected in the surgical period. This study aimed to analyze the effect of BontA on the viability of Random flap in a intra surgical injection. Methods: Twenty male Wistar rats (250–300 g) were randomly divided into four groups: saline injection 15 days prior the surgery (G1), BoNTA injection 15 days prior the surgery (G2), saline injection intraoperative period (G3), BoNTA injection intraoperative (G4). A dorsal cutaneous flap (3×10cm) was performed. Survival area and total area of the flaps were measured. Lumen diameter, external arterial diameter and lumen/wall thickness ratio were recorded. Results: Viable area increased in Bonta 15days group when compared to saline-15days (1080.7 ± 307.5 mm2 vs. 1594.5 ± 419.7mm2, p= 0.01) and in the Bonta –intraoperative injection when compared to saline intraoperative injection (1133.3 ± 462.0 mm2 vs. 1389.9 ± 320.4 mm2, p=0.014). The ratio viable area/total area showed similar results (G1 versus G2, 0.43 vs. 0.74; p<0.001, respectively) and G3 versus G4 (0.44 vs. 0.61 p= 0,04). We did not find any difference in the microscopic analysis (lumen diameter, external arterial diameter and lumen/wall thickness ratio). Conclusion: BoNTA injected fifteen days before the surgery increased skin flap viability. However, BontA injected intraoperatory time did not increased the flap viability.
Evaluation of sarcopenia in long-lived elderly patients: comparison between the muscle mass index and the calf circumference
Authors: Gama Isadora Cecília Salgado , Junior Sergio Chociay , Santana Mariana de Paula , Figueiredo Nadine Motta , Andrade Nathália de Oliveira , Montalvão Gustavo Henrique Martins Rodrigues , Luchesi Bruna  Moretti 
Published: December 2023

Introduction: With population aging, many elderly citizens have been achieving extreme longevity (≥ 90 years). Sarcopenia is related to several adverse outcomes, such as disability, falls, hospitalization and death; hence, its early identification is important. Several methods can be used for its evaluation, with dual-energy x-ray absorptiometry (DXA) being the most accurate. Nevertheless, due to low availability and high cost, other methods are routinely adopted for screening in Primary Health Care (PHC), such as the evaluation of the Muscle Mass Index (MMI) and the Calf Circumference (CC).Objective: To evaluate sarcopenia in elderly people with extreme longevity, and then compare it by means of MMI and CC.Methodology: Cross-sectional and quantitative study, performed in 2019/2020, with n = 69 individuals aged ≥ 90 years, of both genders, users of the Unified Health System in the town of Três Lagoas – MS. We collected sociodemographic and anthropometric data in triplicate. For CC, we used a cutoff score ≤ 31 centimeters as a sign of sarcopenia. We determined MMI based on the calculation of skeletal muscle mass, using the formula of Lee and collaborators, which considers height, body mass, gender, age and ethnicity. The classification of sarcopenia adopted was that of Janssen and collaborators (women: ≤ 5.75 kg/m2 = severe sarcopenia; 5.76 – 6.75 kg/m2 = moderate sarcopenia; and ≥ 6.76 kg/m2 = normal muscle mass. Men: ≤ 8.50 kg/m2 = severe sarcopenia; 8.51 – 10.75 kg/m2 = moderate sarcopenia; and ≥ 10.76 kg/ m2 = normal muscle mass). In order to relate the variables, we applied the Spearman’s correlation test. Results: A total of 52.2% of the participants were women, with an average age of 93.5 years old and 1.3 years of schooling. The average CC was 31.2 centimeters, with 46.1% being considered sarcopenic patients according to this parameter. The average MMI was 5.1 kg/m2, with 100% of the elderly patients being considered sarcopenic through this method. There was no relationship between CC and MMI (p = 0.213).Discussion: We found a high prevalence of sarcopenia in the long-lived elderly patients, mainly using MMI. This data is worrying, since these elderly people may have several limitations due to sarcopenia. The absence of a relationship between the CC and MMI variables highlights the need to use more reliable methods to evaluate sarcopenia in long-lived elderly people, since the identification from CC, despite being easy and fast, may not be sensitive in this age group. Conclusion: We should highlight the need for personalization of public policies and evaluation recommendations for elderly people with extreme longevity in PHC, as they constitute a group that has unique characteristics.
Factors Associated With Tracheostomy in Ventilated Pediatric Trauma Patients. A National Trauma Database Study
Authors: Ahmed Nasim , Kuo Yen-Hong 
Published: December 2023

Purpose The purpose of the study was to find the factors that were associated with tracheostomy procedures in ventilated pediatric trauma patients. Methods The Trauma Quality Improvement Program (TQIP) database of the calendar year 2017 through 2019 was accessed for the study. All patients <18 years old and who were on mechanical ventilation for more than 96 hours were included in the study. Multiple logistic regression analysis was performed to find the factors that were associated with a tracheostomy. Results Out of 2653 patients, 1907 (71.88%) patients underwent tracheostomy. The patients who underwent tracheostomy had a lower median [IQR] of Glasgow Coma Scale (GCS) (3 [3-8] vs 5 [3-10], P < .001) and had a higher proportion of severe spine injury (On Abbreviated Injury Scale [AIS]≥3) (11.6% vs 8.8%, P = .044) when compared with patients who did not have tracheostomy. Lower GCS scores and severe spine injury were associated with higher odds of tracheostomy, with all P values <.05. Higher proportion of tracheostomy procedures were performed at level I pediatric trauma centers as compared to non-designated pediatric centers (odds ratio [95% CI]: 1.848 [1.524-2.242], P < .001). Conclusion A lower GCS score, severe spine injury and highest level trauma centers were associated with a tracheostomy.