bluuebunny/crossref_metadata_2025_split huggingface dataset:
The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania
Authors: Pitta Dipti W. , Indugu Nagaraju , Toth John D. , Bender Joseph S. , Baker Linda D. , Hennessy Meagan L. , Vecchiarelli Bonnie , Aceto Helen , Dou Zhengxia 
Published: December 2020

Abstract
Background
Antimicrobial resistance is a serious concern. Although the widespread use of antimicrobials in livestock has exacerbated the emergence and dissemination of antimicrobial resistance genes (ARG) in farm environments, little is known about whether antimicrobial use affects distribution of ARG in livestock systems. This study compared the distribution of microbiomes and resistomes (collections of ARG) across different farm sectors in dairy herds that differed in their use of antimicrobials. Feces from heifers, non-lactating, and lactating cows, manure storage, and soil from three conventional (antimicrobials used to treat cows) and three organic (no antimicrobials used for at least four years) farms in Pennsylvania were sampled. Samples were extracted for genomic DNA, processed, sequenced on the Illumina NextSeq platform, and analyzed for microbial community and resistome profiles using established procedures.

Results
Microbial communities and resistome profiles clustered by sample type across all farms. Overall, abundance and diversity of ARG in feces was significantly higher in conventional herds compared to organic herds. The ARG conferring resistance to betalactams, macrolide-lincosamide-streptogramin (MLS), and tetracyclines were significantly higher in fecal samples of dairy cows from conventional herds compared to organic herds. Regardless of farm type, all manure storage samples had greater diversity (albeit low abundance) of ARG conferring resistance to aminoglycosides, tetracyclines, MLS, multidrug resistance, and phenicol. All soil samples had lower abundance of ARG compared to feces, manure, and lagoon samples and were comprised of ARG conferring resistance to aminoglycosides, glycopeptides, and multi-drug resistance. The distribution of ARG is likely driven by the composition of microbiota in the respective sample types.

Conclusions
Antimicrobial use on farms significantly influenced specific groups of ARG in feces but not in manure storage or soil samples.
Associations between animal and herd management factors, serological response to three respiratory pathogens and pluck lesions in finisher pigs on a farrow-to-finish farm
Authors: Fitzgerald Rose Mary , O’Shea Helen , Manzanilla Edgar García , Moriarty John , McGlynn Hugh , Calderón Díaz Julia Adriana 
Published: December 2020

AbstractBackgroundSerological screening is a common method to monitor antibody response to pathogen exposure, but results could vary due to several factors. This study aimed to quantify animal and management related factors associated with variation in antibody levels in finisher pigs at slaughter, in an Irish farrow-to-finish farm endemically infected withActinobacillus pleuropneumonia(App),Mycoplasma hyopneumoniae(Mhyo) and swine influenza virus (SIV). A second objective was to estimate differences in antibody levels in pigs presenting pluck lesions. This was an observational study whereby pigs were managed as per routine farm practice. Data on sow parity, number of born alive (NBA) pigs per litter, cross-fostering status, birth and weaning body weight were recorded from 1016 pigs born from one farrowing batch. At slaughter, blood samples were collected for serological analysis and pigs were inspected for presence of enzootic pneumonia (EP)-like lesions, pleurisy, pericarditis and heart condemnations. Pigs were retrospectively classified into three production flows, depending on time spent in each production stage: flow 1 (F1; pigs followed the normal production flow); flow 2 (F2; pigs which were delayed by 1 week from advancing forward); and flow 3 (F3; pigs delayed by > 1 week from advancing forward). A nested case-control design was applied by matching pigs from each flow by sow parity, birth weight and NBA.ResultsPigs born from primiparous sows had higher antibody levels for App than those born to parity ≥5 sows (P < 0.05) and there was no association between any of the pathogens investigated and other early life indicators (P > 0.05). Pigs in F1 had lower antibody levels for App but higher antibody levels for SIV than F2 and F3 pigs (P < 0.05). There was no association between pluck lesions and respiratory pathogens (P > 0.05), except for increased antibody levels for Mhyo when EP-like lesions were present (P = 0.006).ConclusionResults indicate that offspring from primiparous sows develop higher antibody levels for App IV toxin when exposed to this disease and that enforcement of a strict all-in/all-out production system would reduce on-farm disease circulation. A high percentage of pigs were affected with EP-like lesions which were associated with higher antibody levels for Mhyo.
You don’t have to tell a story! A registered report testing the effectiveness of narrative versus non-narrative misinformation corrections
Authors: Ecker Ullrich K. H. , Butler Lucy H. , Hamby Anne 
Published: December 2020

AbstractMisinformation often has an ongoing effect on people’s memory and inferential reasoning even after clear corrections are provided; this is known as the continued influence effect. In pursuit of more effective corrections, one factor that has not yet been investigated systematically is the narrative versus non-narrative format of the correction. Some scholars have suggested that a narrative format facilitates comprehension and retention of complex information and may serve to overcome resistance to worldview-dissonant corrections. It is, therefore, a possibility that misinformation corrections are more effective if they are presented in a narrative format versus a non-narrative format. The present study tests this possibility. We designed corrections that are either narrative or non-narrative, while minimizing differences in informativeness. We compared narrative and non-narrative corrections in three preregistered experiments (totalN = 2279). Experiment 1 targeted misinformation contained in fictional event reports; Experiment 2 used false claims commonly encountered in the real world; Experiment 3 used real-world false claims that are controversial, in order to test the notion that a narrative format may facilitate corrective updating primarily when it serves to reduce resistance to correction. In all experiments, we also manipulated test delay (immediate vs. 2 days), as any potential benefit of the narrative format may only arise in the short term (if the story format aids primarily with initial comprehension and updating of the relevant mental model) or after a delay (if the story format aids primarily with later correction retrieval). In all three experiments, it was found that narrative corrections are no more effective than non-narrative corrections. Therefore, while stories and anecdotes can be powerful, there is no fundamental benefit of using a narrative format when debunking misinformation.
Artificial intelligence and hybrid imaging: the best match for personalized medicine in oncology
Authors: Sollini Martina , Bartoli Francesco , Marciano Andrea , Zanca Roberta , Slart Riemer H. J. A. , Erba Paola A. 
Published: December 2020

AbstractArtificial intelligence (AI) refers to a field of computer science aimed to perform tasks typically requiring human intelligence. Currently, AI is recognized in the broader technology radar within the five key technologies which emerge for their wide-ranging applications and impact in communities, companies, business, and value chain framework alike. However, AI in medical imaging is at an early phase of development, and there are still hurdles to take related to reliability, user confidence, and adoption. The present narrative review aimed to provide an overview on AI-based approaches (distributed learning, statistical learning, computer-aided diagnosis and detection systems, fully automated image analysis tool, natural language processing) in oncological hybrid medical imaging with respect to clinical tasks (detection, contouring and segmentation, prediction of histology and tumor stage, prediction of mutational status and molecular therapies targets, prediction of treatment response, and outcome). Particularly, AI-based approaches have been briefly described according to their purpose and, finally lung cancer—being one of the most extensively malignancy studied by hybrid medical imaging—has been used as illustrative scenario. Finally, we discussed clinical challenges and open issues including ethics, validation strategies, effective data-sharing methods, regulatory hurdles, educational resources, and strategy to facilitate the interaction among different stakeholders. Some of the major changes in medical imaging will come from the application of AI to workflow and protocols, eventually resulting in improved patient management and quality of life. Overall, several time-consuming tasks could be automatized. Machine learning algorithms and neural networks will permit sophisticated analysis resulting not only in major improvements in disease characterization through imaging, but also in the integration of multiple-omics data (i.e., derived from pathology, genomic, proteomics, and demographics) for multi-dimensional disease featuring. Nevertheless, to accelerate the transition of the theory to practice a sustainable development plan considering the multi-dimensional interactions between professionals, technology, industry, markets, policy, culture, and civil society directed by a mindset which will allow talents to thrive is necessary.
Apolipoproteins A1 and B and their ratio in acute ischemic stroke patients with intracranial and extracranial arterial stenosis: an Egyptian study
Authors: Fahmy Ebtesam Mohammed , El Awady Mohammed Ahmed El Sayed , Sharaf Sahar Abdel-Atty , Selim Nora Mahmoud , Abdo Hazem El Sawy , Mohammed Shaimaa Shaheen 
Published: December 2020

Abstract
Background
Apolipoprotein A1 and B and their ratio are considered a better biomarker for cardiovascular diseases than a lipid profile, but this previous finding is not proved to cerebrovascular ischemic diseases. The aim of this study is to assess the relation between apolipoprotien A1 and B and their ratio to intra- and extracranial carotid atherosclerosis in patients with ischemic acute stroke.

Methods
90 Egyptian patients with acute ischemic stroke are included in the study, and they have been classified into 3 groups: group 1 includes 30 patients with intracranial stenosis, group 2 includes 30 patients with extracranial arterial stenosis, and group 3 includes 30 patients with non-arterial stenosis. Patients were subjected to clinical assessment, routine laboratory measures, and Color-Coded Duplex Sonography for extracranial and intracranial arteries. The measurement of serum levels of apolipoproteins A1 and B was done using enzyme-linked immuno-sorbent assay (ELISA).

Results
A statistically significant difference was found between patient groups as regards the frequency of abnormal serum LDL-cholesterol (p = 0.04), being elevated in patients with extracranial stenosis (p = 0.01). There was a significant difference between patients groups as regards the frequency of abnormal serum HDL-cholesterol (p = 0.02), being lower in patients with extracranial stenosis. High Apo B/A1 ratio was an independent risk factor for intracranial arterial stenosis (p = 0.045). An abnormal elevation of serum LDL cholesterol was an independent risk factor of extracranial arterial stenosis (p = 0.021).

Conclusion
Apo B/A1 ratio is an independent risk factor for intracranial arterial stenosis, while serum LDL cholesterol is an independent risk factor for extracranial arterial stenosis. Apo B/A1 ratio and serum LDL cholesterol are reliable serum biomarkers for cranial arterial stenosis in acute ischemic stroke patients.
Antimicrobial activity of Syzygium aromaticum L. essential oil on extended-spectrum beta-lactamases-producing Escherichia coli
Authors: Mejía-Argueta E. L. , Santillán-Benítez J. G. , Canales-Martinez M. M. , Mendoza-Medellín A. 
Published: December 2020

AbstractBackgroundTo test the antimicrobial potential of clove essential oil that has been less investigated on antimicrobial-resistant organisms (extended-spectrum β-lactamase-ESBL-producingEscherichia coli),we collected 135 ESBL-producingEscherichia colistrains given thatE. coliis the major organism increasingly isolated as a cause of complicated urinary and gastrointestinal tract infections, which remains an important cause of therapy failure with antibiotics for the medical sector. Then, in this study, we evaluated the relationship between the antibacterial potential activity ofSyzygium aromaticumessential oil (EOSA) and the expression of antibiotic-resistant genes (SHV-2, TEM-20) in plasmidic DNA on ESBL-producingE. coliusing RT-PCR technique.ResultsEOSA was obtained by hydrodistillation. Using Kirby-Baüer method, we found that EOSA presented a smaller media (mean = 15.59 mm) in comparison with chloramphenicol (mean = 17.73 mm). Thus, there were significant differences (p < 0.0001). Furthermore, EOSA had an antibacterial activity, particularly on ECB132 (MIC: 10.0 mg/mL and MBC: 80.0 mg/mL), and a bacteriostatic effect by bactericidal kinetic. We found that the expression of antibiotic-resistant gene blaTEM-20 was 23.52% (4/17 strains) and no expression of blaSHV-2. EOSA presented such as majority compounds (eugenol, caryophyllene) using the GC–MS technique.ConclusionsPlant essential oils and their active ingredients have potentially high bioactivity against a different target (membranes, cytoplasm, genetic material). In this research, EOSA might become an important adjuvant against urinary and gastrointestinal diseases caused by ESBL-producingE. coli.
Detection of tmprss2-erg and tmprss2-egr1 gene fusion in prostate cancer from a Chinese population
Authors: Xu Changqing , Luo Jindan , Wang Mengmeng , Wang Yin , Chen Zhaojing , Cao Yifei , Hong Yu , Xu Xianrong , Yang Jun 
Published: December 2020

Abstract
Background
TMPRSS2: ETS gene fusion occurs recurrently in a high proportion of prostate cancer (PCa) patients in Western countries. However, for Chinese PCa patients, no solid conclusion could be drawn from the present studies, as the results varied considerably between the limited reports.

Results
In this study, we evaluated the prevalence of such gene rearrangements in a small number of Chinese PCa patients and discovered that 6 out of 27 (22.2%) were found to harbor the TMPRSS2: ERG fusion, the ratio was much lower than that in Western countries. Furthermore, we first identified TMPRSS2: EGR1 gene fusion, suggesting other chromosome rearrangements besides ETS gene family harbor in prostate cancer. The hybrid transcript was predicted to encode a truncated EGR1 protein by ORF finder, which might play a key role in prostate cancer.

Conclusions
We reported that the total occurrence rate of TMPRSS2: ERG fusion gene in this small group of Chinese patients was lower than the reported frequencies in European descent patients but comparable to other reported frequencies in Asian populations. The occurrence of TMPRSS2: EGR1 gene fusion suggested other chromosome rearrangements in prostate cancer.
Longitudinal assessment of chest computerized tomography and oxygen saturation for patients with COVID-19
Authors: Osman Ahmed M. , Farouk Suzan , Osman Nehad M. , Abdrabou Ahmed M. 
Published: December 2020

Abstract
Background
COVID-19 is a pandemic disease and is important to know the nature of the disease during follow-up. We aimed to study different imaging signs and changes that occurred during the initial scan, follow-up, and complications. Moreover, to study the CT severity score and its relation to the patients’ clinical condition using oxygen saturation as a parameter. This was a retrospective study conducted on 125 patients, including 293 CT studies, from March till the end of August 2020. The mean age was 47.4 ± 15.7 years and 64.8% of the patients were males. All patients proved to have COVID-19 by the RT-PCR test. The CT studies of the patients were divided into four stages according to the timing after the onset of symptoms. The incidence of different CT features, patterns, complications, CT severity score, and oxygen saturation were recorded in different stages.

Results
During follow-up studies, GGOs were the most constant and common CT features. Consolidation and crazy paving showed gradual progression to reach the peak at the 3rd stage. Mixed attenuation pattern was the commonest pattern at the 3rd stage while a pure GGO pattern was the commonest feature in other stages. The complications occurred mostly in the 3rd stage. Nevertheless, the CT severity score showed an inverse relation with oxygen saturation.

Conclusion
Radiological evaluation of COVID-19 pneumonia showed gradual progression till the peak critical stage at 8-14 days from the onset of symptoms. Consolidation and mixed attenuation pattern can be considered as CT signs of disease severity.
Molecular identification and antimicrobial activity of endophytic fungi isolated from Heritiera fomes (Buch. -Ham), a mangrove plant of the Sundarbans
Authors: Nurunnabi Tauhidur Rahman , Sarwar Sabiha , Sabrin Farah , Alam Farzana , Nahar Lutfun , Sohrab Hossain , Sarker Satyajit D. , Rahman S. M. Mahbubur , Billah Morsaline 
Published: December 2020

Abstract
Background
Endophytic fungi play a vital role in plant defense system by secreting various antimicrobial agents. To evaluate the antimicrobial activity of the endophytic fungi of the mangrove plant Heritiera fomes (Buch. -Ham), plants were collected from the Sundarbans, Bangladesh. The endophytic fungi were subsequently isolated and identified.

Results
Fifty-five endophytic fungi were isolated from the leaves, root, and bark of H. fomes (Buch. -Ham). Genomic DNA was extracted for PCR (polymerase chain reaction) by specific primers to multiply ITS region and sequences were determined. Nucleotide sequence data were submitted to the Genbank and accession number for each fungal strain was obtained. Antimicrobial activity of the ethyl acetate (EtOAc) and methanolic extracts of eleven species from both fermentation and mycelium, respectively, were analyzed by microtiter plate-based antimicrobial assay incorporating resazurin as an indicator of cell growth against two Gram-positive bacteria namely Staphylococcus aureus NCTC 12981 and Micrococcus luteus NCTC 7508, two Gram-negative bacteria namely Escherichia coli NCTC 12241 and Pseudomonas aeruginosa NCTC 12903, and a fungus Candida albicans ATCC 90028. All the endophytic fungal extracts exhibited antimicrobial activities against more than one-tested pathogenic microbial strains. Overall, methanolic extracts showed greater activity than EtOAc extracts. Pseudopestalotiopsis camelliae-sinensis, Pestalotiopsis microspora, and Penicillium copticola were the most active endophytic fungal strains and exhibited strong inhibitory activity against the microorganisms under investigation and their MIC values ranged from 0.0024 to 5.0 mg/mL. Methanolic extracts of both P. camelliae-sinensis and P. microspora showed the highest antibacterial activity (MIC value of 0.0024 mg/mL) against P. aeruginosa NCTC 12903.

Conclusion
This study showed that the isolated and identified endophytic fungi from H. fomes (Buch. -Ham) could be potential sources of antimicrobial agents.
Synthesis, in silico studies and antibacterial activity of some novel 2-substituted benzimidazole derivatives
Authors: Chintakunta Ramakrishna , Meka Geethavani 
Published: December 2020

Abstract
Background
The o-phenylenediamine is a versatile starting material for several compounds. Synthesized o-phenylenediamine and amino acids (glycine, alanine, aspartic acid, and l-proline) undergo condensation via Phillips reaction. The synthesized compound showed the promising antibacterial activity of Bacillus subtilis and Pseudomonas aeruginosa at the concentration of 100, 50, 25, 12.5, 6.25, 3.12, 1.6, 0.8, 0.4, and 0.2 μg/ml. Ciprofloxacin was used as standard drug. Synthesis of benzimidazole derivatives was carried out and purified by recrystallization process using ethanol. Substituted derivatives were characterized by melting point, TLC and spectroscopic methods include FT-IR and 1H-NMR.

Results
In silico studies were adopted for synthetic derivatives by Molinspiration, ChemDraw, and online software tool. Minimum inhibitory concentration (MIC) values of B. subtilis and P. aeruginosa were reported, and benzimidazole ligands and Molinspiration scores were generated and listed.

Conclusion
The more negative values indicate a higher binding affinity. The generated ligand observations can be visualized. Physical constants of synthesized derivates such as solubility and melting point were determined. Bioactivity scores were noted for different derivatives and predicted percentage absorption in the gut. The antibacterial activity was performed using the MIC method (aerobic).
Symptomatic prostatic utricle: various approaches for treatment
Authors: S. Manjiri , Luthra Kush , S. K. Padmalatha , Shetty Jeevak , Patil Neehar 
Published: December 2020

Abstract
Background
Pediatric presentations of a prostatic utricle have received only little attention. The incidence of symptomatic prostatic utricle has been reported but most cases are asymptomatic. The purpose of this study is to highlight the various clinical presentations and surgical approaches to treat a symptomatic prostatic utricle.

Results
This study includes a series of 7 cases over a period of 5 years. The diagnosis of prostatic was made on the basis of clinical presentations, ultrasonography, micturating cystourethrogram, and cystoscopy.
Of the 7 patients, the newborn patient had antenatally detected abdominal cystic mass which presented with postnatal urinary retention, 5 patients had various urinary complaints, and 1 older child with disorder of sexual differentiation (DSD) had urinary incontinence. Depending upon the grade of prostatic utricle, treatment was done in the form of laparoscopic-assisted excision in 1, laparotomy and excision in 1, perineal excision in 2, and cystoscopic fulguration in 3 patients. Postoperative period was uneventful. All the patients were followed for a period of 1–2 years. Most of them were asymptomatic except one child who had recurrent episodes of epidydimo orchitis which was treated conservatively, and he was also asymptomatic at the end of 1 year. Five patients who had associated hypospadias were observed for one year for any urinary complaints before they underwent definitive repair for hypospadias.

Conclusion
Prostatic utricle is a vestigial remnant of müllerian duct most commonly associated with posterior hypospadias. High index of suspicion for prostatic utricle in cases with recurrent urinary complaints helps in timely detection and appropriate treatment can prevent further complications. Cystoscopy and micturating cytourethrogram remains the gold standard for diagnosis.