syedzayyan/paper_mill_benchmark huggingface dataset:
Shigella sonnei: virulence and antibiotic resistance.

Shigella sonnei is the emerging pathogen globally, as it is the second common infectious species of shigellosis (bloody diarrhoea) in low- and middle-income countries (lmics) and the leading one in developed world.The multifactorial processes and novel mechanisms have been identified in s.Sonnei, that are collectively playing apart a substantial role in increasing its prevalence, while replacing the s.Flexneri and other gram-negative gut pathogens niche occupancy.Recently, studies suggest that due to improvement in sanitation s.Sonnei has reduced cross-immunization from plesiomonas shigelliodes (having same o-antigen as s.Sonnei) and also found to outcompete the two major species of enterobacteriaceae family (shigella flexneri and escherichia coli), due to encoding of type vi secretion system (t6ss).This review aimed to highlight s.Sonnei as an emerging pathogen in the light of recent research with pondering aspects on its epidemiology, transmission, and pathogenic mechanisms.Additionally, this paper aimed to review s.Sonnei disease pattern and related complications, symptoms, and laboratory diagnostic techniques.Furthermore, the available treatment reigns and antibiotic-resistance patterns of s.Sonnei are also discussed, as the ciprofloxacin and fluoroquinolone-resistant s.Sonnei has already intensified the global spread and burden of antimicrobial resistance.In last, prevention and controlling strategies are briefed to limit and tackle s.Sonnei and possible future areas are also explored that needed more research to unravel the hidden mysteries surrounding s.Sonnei.

Journal: Archives of microbiology (2021)
Publication types: Journal Article;Review
Polyploid progeny from triploid hybrids of Phegopteris decursivepinnata (Thelypteridaceae).

Phegopteris decursivepinnata includes diploids, tetraploids, and triploid hybrids based on x = 30.We obtained polyploid progeny from triploid hybrids through selfing and crossing experiments.Triploids occasionally formed well-filled spores.The mean occurrence frequencies of well-filled and germinated spores were 2.8% and 0.8%, respectively.Viable spores that succeeded in germinating were regarded as unreduced, triploid spores, because the resulting gametophytes yielded triploid (2n = 86-92) and hexaploid (2n = 170-184) progeny in both isolated and mixed cultures of gametophytes.The triploid and hexaploid progeny likely arose apogamously and sexually, respectively.One of the hexaploid progeny yielded hexaploid sporophytes (2n = 169-180) in the mixed culture of its gametophytes.Artificial crossing between triploid and diploid sporophytes produced tetraploid (2n = 116, 120) and pentaploid (2n = 145-150) progeny that likely arose through the mating of 3x gametes from the triploid with both 1x and 2x gametes from the diploid, respectively.Unreduced spore formation was confirmed in diploid sporophytes.The tetraploid progeny formed viable spores at a frequency of 63-75%.Triploid hybrids of this species are thus expected to produce new triploids, tetraploids, and hexaploids in nature.The wide range of variation in chromosome numbers of hexaploid progeny suggests that viable spores from parental triploid hybrids had unreduced chromosomes, whose numbers, however, deviated considerably from those of the hybrids.This chromosome deviation of viable spores may result from errant movements of chromatids of univalents when unreduced dyads form in meiosis.Downward chromosome deviation from the chromosome number of the parental hybrids may affect the developmental progress of viable spores more tolerantly than upward chromosome deviation.

Journal: Journal of plant research (2021)
Publication types: Journal Article
LOW VULNERABILITY OF THE POSTERIOR EYE SEGMENT TO SARS-COV-2 INFECTION: Chorioretinal SARS-CoV-2 Vulnerability.

Retinal manifestations have been described in covid-19 patients, but it is unknown whether sars-co v-2, the causal agent in covid-19, can directly infect posterior ocular tissues.Here, we investigate sars-co v-2 host factor gene expression levels and their distribution across retinal and choroidal cell types.Methods query of single-cell rna sequencing data from human retina and choroid.Results we find no relevant expression of two key genes involved in sars-co v-2 entry, ace2 and tmprss2, in retinal cell types.By contrast, scarce expression levels could be detected in choroidal vascular cells.Conclusion given the current understanding of viral host cell entry, these findings suggest a low vulnerability of the posterior eye segment to sars-co v-2 with a potential weak spot in the vasculature, which could play a putative causative role in ocular lesions in covid-19 patients.This may qualify the vasculature of the human posterior eye segment as an in vivo biomarker for life-threatening vascular occlusions in covid-19 patients.

Journal: Retina (Philadelphia, Pa.) (2022)
Publication types: Journal Article
Paranoid and misidentification subtypes of psychosis in dementia.

This study aimed to review the neurobiological and neuropsychological correlates of paranoid (persecutory delusions) and misidentification (misidentification delusions and/or hallucinations) subtypes of psychosis in dementia, to establish if they represent distinct subphenotypes.Nine studies were eligible, all included patients with alzheimer's disease.Greater global cognitive deficits and an accelerated global cognitive decline were observed in the misidentification subtype.Neuroimaging studies showed more marked volume loss in multiple regions in patients with the misidentification subtype, including those involved in object recognition and the processing of information on spatial and temporal context.A single study found greater impairment in visual sustained attention and object recognition in the misidentification subtype.The small number of studies and methodological heterogeneity limit interpretation of the findings.Nevertheless, these findings would tentatively suggest that there may be additional or accelerated pathological change in functional networks involved in visuoperceptual processing in the misidentification subtype.This should be further explored in prospective studies and the investigation extended to other forms of dementia, to gain a transdiagnostic perspective.

Journal: Neuroscience and biobehavioral reviews (2022)
Publication types: Journal Article;Review
Nuclear Factor κB Signaling and Its Related Non-coding RNAs in Cancer Therapy.

Nuclear factor κb (nf-κb) acts as a nuclear factor that is composed of five main subunits.It is a pluripotent and crucial dimer transcription factor that has a close relationship with many serious illnesses, especially its influences on cell proliferation, inflammation, and cancer initiation and progression.Nf-κb acts as part of the signaling pathway and determines its effect on the expression of several other genes, such as epidermal growth factor receptor (egfr), p53, signal transducer and activator of transcription 3 (stat3), and non-coding rna (nc rna).Continuous activation of the nf-κb signaling pathway has been seen in many cancer types.While the nf-κb signaling pathway is tightly regulated in physiological settings, quite frequently it is constitutively activated in cancer, and the molecular biology mechanism underlying the deregulated activation of nf-κb signaling remains unclear.In this review, we discuss the regulatory role and possible clinical significance of nc rna (micro rna [mi rna] and long non-coding rna [lnc rna]) in nf-κb signaling in cancer, including in the conversion of inflammation to carcinogenesis.Non-coding rna plays an essential and complex role in the nf-κb signaling pathway.Nf-κb activation can also induce the nc rna status.Targeting nf-κb signaling by nc rna is becoming a promising strategy of drug development and cancer treatment.

Journal: Molecular therapy. Nucleic acids (2020)
Publication types: Journal Article;Review
Nasoethmoid orbital fracture reconstruction using a three-dimensional printing-based craniofacial plate.

The face is one of the most important parts of the body.Untreated facial fractures can result in deformities that can be harmful to patients.Three-dimensional (3d) printing is a rapidly evolving technology that has recently been widely applied in the medical field as it can potentially improve patient treatment.Although 3d printing technology is mostly used for craniofacial surgery, some studies have proved that it can be used to treat nasoethmoid orbital fractures.In this study, a patient-customized plate was constructed using a 3d printer and applied in a simulated surgery for the treatment of nasoethmoid orbital fracture.

Journal: Archives of craniofacial surgery (2022)
Publication types: Journal Article
Providing HIV testing in men who have sex with men through a gay social networking app in China: A qualitative interview study with multisectoral service providers.

We explored the feasibility of app-based hiv testing services (ahts) among men who have sex with men (msm) according to the perspectives of testing service providers.Methods twenty-one current or previous ahts providers participated in a semi-structured interview which explored the facilitators and barriers to ahts.Ten participants originating from the center for disease control and prevention (cdc) and 11 from the non-governmental organization (ngo) in shijiazhuang, china took part in this study.Interviews was transcribed verbatim, and the socioecological model (sem) was applied to thematic analysis.Results twenty-one participants from ahts services commented on the integration of online appointment schedules into hiv testing services.Ahts was deemed a convenient and efficient method for msm and service providers to choose their preferred location and times.Moreover, it allowed for important hiv-related information to be accessed online and targeted toward at-risk individuals.Participants thought msm may feel unsure about personal information security being stored within a privatized app and was considered a barrier to ahts's usability.As such, they believed establishing a government-led national online platform for ahts would allow for greater trust from msm, rather than a social media app.Conclusion by linking booking services to an online platform, ahts was deemed a convenient and efficient method for hiv testing services, especially for young msm who are familiar with smartphone applications.To improve the use of these services, ahts apps should focus on ensuring the confidentiality of personal information and internet security to build trust between msm and service providers.

Journal: Frontiers in public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Gram-Negative Bacteria Bloodstream Infections in Patients with Hematological Malignancies - The Impact of Pathogen Type and Patterns of Antibiotic Resistance: A Retrospective Cohort Study.

Enterobacteriaceae(eb) and non-fermentative bacteria (nfb) are the main pathogens responsible for gram-negative bloodstream infections (gn-bsi) in patients with hematological malignancies (hms).These two pathogen types have heterogeneous resistance mechanisms to antibiotics.However, the impact of pathogen species and pattern of antibiotic resistance on the outcomes of patients with hms remains unclear.Methods we retrospectively collected clinical data of patients with hms at three comprehensive hospitals in hunan province, china, between january 2010 and may 2018.The data analyzed the impact that different species and patterns of antibiotic resistance had on the outcome of patients with hms.Results the majority of the 835 monomicrobial isolates collected from patients with hms and gn-bsis were enterobacteriaceae(75.7%).While detections of mdr pathogens in bsis as a whole are decreasing, sub-analysis shows that detections of extended spectrum β-lactamase-producing (esbl)enterobacteriaceaeand carbapenem-resistant pathogens in biss are rising.Comparing different species, the early mortality rate associated with infections caused by nfb was significantly higher than infections caused by enterobacteriaceae(22.6% vs 9.7%, p < 0.001).Across different multidrug-resistant (mdr) patterns, esbl bacteria did not have a significant impact on health outcomes.Carbapenem-resistant bacteria, on the other hand, were observed to significantly affect early mortality rate, such as carbapenem-resistant klebsiella pneumoniae(36.0% vs 7.6%, p < 0.001) and carbapenem-resistant non-fermentative bacteria (44.7% vs 16.5%, p < 0.001).Conclusion our findings suggest that both species and patterns of antibiotic resistance can affect the early mortality of patients with hms during bsi.

Journal: Infection and drug resistance (2021)
Publication types: Journal Article
Palliative home-based care to pediatric cancer patients: characteristics and healthcare delivered.

S cancer patients constitute an important group in pediatric palliative care.Though the patients' home is the preferred place of care, little is known about the characteristics of patients attended by units that provide home assistance.Our objective is to describe the characteristics of cancer patients and healthcare delivered by a pediatric palliative care unit with a home hospitalization program.Methods retrospective study based on clinical records of deceased patients attended by the pediatric palliative care unit of madrid over 10 years.Data collected included general characteristics, type of cancer, whether they received home assistance, place of death, healthcare delivered (hospitalizations, devices, oncological treatments...), and symptom prevalence.Results after excluding 47 patients, the clinical records of 144 patients were analyzed.The median age at referral was 9.4 years (iqr: 5.6-14.1), 61.2% were males; 44.2% had solid non-cns tumors, 35.4% cns tumors, and 20.4% hematological malignancies; 137 received home care with 89 not requiring further hospital admissions and 70.1% dying at home.The median follow-up time was 1.6 months (iqr: 0.5-2.9).The most used devices were venous ports (71.4%) and oxygen (49.4%); 53.5% of the patients received oncological support therapies.The most common symptoms were pain (91.8%) dyspnea (49.0%) and fatigue (46.9%).Conclusions home assistance was provided in a high number of patients, with a large proportion needing one or no hospital admissions and 70.1% of them dying at home.Further studies characterizing these patients and the factors which promote early access to palliative care are needed.

Journal: Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer (2022)
Publication types: Journal Article
Can we reduce dose to ureters as avoidance organs for MRI based brachytherapy for cervical cancer? A dosimetric feasibility study.

And purpose ureteral stenosis (us) is an underreported complication of brachytherapy (bt) for cervical cancer (cc), with limited data on toxicity risk reduction.A previous study demonstrated ureter eqd2 d0.1cc > 77 gy correlated with us development.We sought to assess feasibility of this constraint while maintaining similar hr-ctv coverage.Materials and methods patients with locally advanced cc treated with ebrt plus hdr mri-based brachytherapy boost without hydronephrosis at diagnosis and with ureter dose eqd2 d0.1cc > 77 gy were included.Replan was attempted to achieve hr-ctv d90 ≥ 80-85 gy and ureter dose reduction.Ureter distance from lateral margin of hr-ctv and tandem was recorded.T-test was performed to compare ureteral dose and hr-ctv d90.Results of 25 patients were identified.Hundred percent received 45 gy in 25 fractions to the pelvis ± paraaortic lymph nodes and 80% receiving median additional parametrial dose of 5.4 gy.Replan meeting ureteral dose of ≤77 gy was feasible in 18 of 25 patients, with a reduction in median ureter d0.1cc from 82.3 to 76.8 gy (p < 0.001).Median hr-ctv d90 was similar (84.7 vs.85.0 gy).Replan achieved d0.1cc ≤77 gy in 56% of patients who experienced us.All unilateral us cases occurred in the ureter closest to hr-ctv.Conclusions optimization to reduce ureter dose to ≤77 gy is feasible when ureters are visible and contoured.Ureters may be considered as potential oar during mri-based brachytherapy treatment.Reduced ring to tandem total reference air kerma (trak) ratio may provide an additional metric by which to lower us risk.

Journal: Brachytherapy (2022)
Publication types: Journal Article
BULBOSITIES AND INTERVORTEX VENOUS ANASTOMOSIS IN VENOUS OVERLOAD CHOROIDOPATHY MASQUERADING AS POLYPOIDAL CHOROIDAL VASCULOPATHY.

To describe a patient with venous overload choroidopathy in whom venous bulbosities masqueraded as polyps and intervortex venous anastomosis mimicked a branching vascular network, giving the appearance of polypoidal choroidal vasculopathy.Methods the patient had complete ophthalmic examination including indocyanine green angiography and optical coherence tomography.Venous bulbosities were defined on indocyanine green angiography as focal dilations in which the diameter of the dilation is two times that of the host vessel.Results a 75-year-old woman presented with combined subretinal and subretinal pigment epithelium hemorrhages in the right eye.During indocyanine green angiography, focal nodular hyperfluorescent lesions connected to a network of vessels were observed, which looked like polyps and branching vascular network in polypoidal choroidal vasculopathy.In both eyes, the midphase angiogram had multifocal choroidal vascular hyperpermeability.There was late-phase placoid staining nasal to the nerve in the right eye.During enhanced depth imaging-optical coherence tomography evaluation, there were no retinal pigment epithelium elevations that would be expected with polyps or branching vascular network in the right eye.A double-layer sign was seen corresponding to the placoid area of staining.Diagnosis of venous overload choroidopathy and choroidal neovascularization membrane was made.She was treated with intravitreal antivascular endothelial growth factor injections for the choroidal neovascularization membrane.Conclusion indocyanine green angiography findings in venous overload choroidopathy may mimic polypoidal choroidal vasculopathy, but differentiation is essential because it has implications for treatment.Similar findings may have been misinterpreted in the past and may have previously contributed to conflicting clinical and histopathologic descriptions of polypoidal choroidal vasculopathy.

Journal: Retinal cases & brief reports (2024)
Publication types: Journal Article;Case Reports
Microbial Communities in Retail Draft Beers and the Biofilms They Produce.

In the beer brewing industry, microbial spoilage presents a consistent threat that must be monitored and controlled to ensure the palatability of a finished product.Many of the predominant beer spoilage microbes have been identified and characterized, but the mechanisms of contamination and persistence remain an open area of study.Postproduction, many beers are distributed as kegs that are attached to draft delivery systems in retail settings where ample opportunities for microbial spoilage are present.As such, restaurants and bars can experience substantial costs and downtime for cleaning when beer draft lines become heavily contaminated.Spoilage monitoring on the retail side of the beer industry is often overlooked, yet this arena may represent one of the largest threats to the profitability of a beer if its flavor profile becomes substantially distorted by contaminating microbes.In this study, we sampled and cultured microbial communities found in beers dispensed from a retail draft system to identify the contaminating bacteria and yeasts.We also evaluated their capability to establish new biofilms in a controlled setting.Among four tested beer types, we identified over a hundred different contaminant bacteria and nearly 20 wild yeasts.The culturing experiments demonstrated that most of these microbes were viable and capable of joining new biofilm communities.These data provide an important reference for monitoring specific beer spoilage microbes in draft systems and we provide suggestions for cleaning protocol improvements.importancebeer production, packaging, and service are each vulnerable to contamination by microbes that metabolize beer chemicals and impart undesirable flavors, which can result in the disposal of entire batches.Therefore, great effort is taken by brewmasters to reduce and monitor contamination during production and packaging.A commonly overlooked quality control stage of a beer supply chain is at the retail service end, where beer kegs supply draft lines in bars and restaurants under nonsterile conditions.We found that retail draft line contamination is rampant and that routine line cleaning methods are insufficient to efficiently suppress beer spoilage.Thus, many customers unknowingly consume spoiled versions of the beers they consume.This study identified the bacteria and yeast that were resident in retail draft beer samples and also investigated their abilities to colonize tubing material as members of biofilm communities.

Journal: Microbiology spectrum (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Frequently assessed and used prognostic factors for outcome after macular hole surgery: which is better?

The aim of this retrospective study was to evaluate commonly used clinical and oct-morphological parameters, including perifoveal pseudocysts, as prognostic factors for postoperative outcome after macular hole surgery in a retinal referral clinic in north rhine-westphalia, germany.Methods and material this was a retrospective analysis of all patients who underwent surgery because of idiopathic mh between 2011 and 2017 in augenklinik tausendfensterhaus, duisburg, germany.Statistical evaluation of clinical and oct-based parameters, including the areas of intraretinal pseudocysts, was conducted.The main statistical outcomes were surgical success and visual acuity.Only parameters with a highly significant correlation to the outcome parameters (postoperative visual acuity (va); surgical success) in univariate analysis were entered in linear and logistic regression analyses.Results a total of 189 eyes of 178 patients (71.4% female; mean age 67.5 ± 8.2 a) who underwent surgery because of mh were included.The overall closure rate was 86.8%.The mean best corrected va increased from 0.7 ± 0.3 log mar before surgery to 0.5 ± 0.3 log mar (p < 0.0001).While several clinical and oct-based parameters as well as calculated indices showed a significant correlation with the outcome measures, the regression analysis showed that the minimum linear diameter was the only parameter that both predicted surgical success (p = 0.015) and was correlated with postoperative va (p < 0.001).Conclusion the minimum linear diameter serves as an easily assessed prognostic factor with the best predictive properties.This result is of great importance for clinical practice, as it simplifies the postsurgical prognosis.

Journal: BMC ophthalmology (2021)
Publication types: Journal Article