Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission

Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173 high-quality SARS-CoV-2 genomes. We integrated patient movement and staff location data into the analysis of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples. Incorporation of HCW location further increased the number of individuals within PCCs and identified additional links in SARS-CoV-2 transmission pathways. Patients within PCCs carried viruses more genetically identical to HCWs in the same ward location. SARS-CoV-2 genome sequencing integrated with patient and HCW movement data increases identification of outbreak clusters. This dynamic approach can support infection control management strategies within the healthcare setting.
HPLC and Mass Spectrometric Analysis of Carotenoids from Mango

β-Carotene (all-trans), β-cryptoxanthin (all-trans and cis), zeaxanthin (all-trans), luteoxanthin isomers, violaxanthin (all-trans and cis), and neoxanthin (all-trans and cis) were identified in mango cultivar Keitt by means of HPLC data (retention time, co-injection, and chemical reactions). Mass spectrometry (molecular ion, fragmentation pattern, m/z relative intensity) confirmed the identity of these carotenoids (not the geometric form); additionally, lutein and mutatochrome were detected when a large amount of sample was utilized. The quantitative composition was determined by HPLC, Sudan I being used as internal standard. all-trans-Violaxanthin (21.1 ± 2.9 μg/g), all-trans-β-carotene (15.1 ± 1.5 μg/g), and a cis-violaxanthin (10.1 ± 0.2 μg/g), tentatively identified as 9-cis, were the principal carotenoids. Keywords: Mango carotenoids; HPLC; MS
Long-Term Orthophosphate Removal in a Field-Scale Storm-Water Bioinfiltration Rain Garden

AbstractUnabated runoff from impervious surfaces after rain events is considered a major source of impairment of receiving water bodies. Bioinfiltration storm-water control measures (SCM) have been shown to be effective in reducing runoff and pollutants from urban areas and thus provide a mechanism for protecting downstream sources from erosion and contamination from suspended solids, metals, and nutrients. However, less is known about the loss mechanisms responsible for contaminant removal and the long-term performance of such SCMs. Even less is known of the performance from a vadose zone perspective. The research presented herein examines the long-term (9 year) performance of a bioinfiltration rain garden with specific emphasis on the removal of orthophosphate. Field data indicated clear removal trends for orthophosphate (PO43−P), the bioavailable form of phosphorus, as the storm water infiltrated into the infiltration bed of the rain garden. The median PO43−P concentration decreased from 0.21–0.25 mg/.
Breast Milk Virome and Bacterial Microbiome Resilience in Kenyan Women Living with HIV

Breastfeeding plays an important role in seeding the infant gut microbiome and mammary health. Although most studies focus on the diverse breast milk bacterial communities, little is known about the viral communities harbored in breast milk. ABSTRACT Breast milk is nutritionally and immunologically beneficial in early life but is also a potential source of infection. Little is known about breast milk microbiota of women living with HIV (WLHIV), the impact of severe immunosuppression, and the contribution to mortality of HIV-exposed infants. Here, we performed metagenomic sequencing to characterize the bacterial microbiome and DNA virome of breast milk samples at 1 month postpartum from Kenyan WLHIV who were not receiving combination antiretroviral therapy (cART), 23 women with CD4 counts of <250 and 30 women with CD4 of >500; and additionally, 19 WLHIV with infants that lived and 26 WLHIV with infants that died during the first 2 years of life were included. We found that breast milk bacterial microbiomes in this study population were highly diverse but shared a core community composed of the Streptococcaceae, Staphylococcaceae, Moraxellaceae, and Eubacteriaceae families. The breast milk virome was dominated by human cytomegalovirus (CMV) and included the bacteriophage families Myoviridae, Siphoviridae, and Podoviridae. Bacterial microbiome and virome profiles and diversity were not significantly altered by HIV immunosuppression, as defined by a CD4 of <250. CMV viral load was not associated with maternal CD4 counts or infant mortality. In conclusion, we show that the core bacterial and viral communities are resilient in breast milk despite immunosuppression in WLHIV. IMPORTANCE Breastfeeding plays an important role in seeding the infant gut microbiome and mammary health. Although most studies focus on the diverse breast milk bacterial communities, little is known about the viral communities harbored in breast milk. We performed the first breast milk virome study of an HIV population. In this study cohort of Kenyan women living with HIV from the pre-antiretroviral therapy era, we found that breast milk harbors a core bacterial microbiome and a virome dominated by human cytomegalovirus. The virome and bacterial microbiome were not substantially altered by immunosuppression or associated with infant mortality. Together, these findings indicate resilience of the microbial community in breast milk compartmentalization. These findings advance out fundamental understanding of the breast milk core microbiome and virome interactions in the context of HIV disease.
Efficacy of progressive thickness intrastromal corneal ring segments in the treatment of duck phenotype keratoconus

Purpose: To evaluate clinical outcomes in patients with asymmetric duck phenotype keratoconus implanted with asymmetric progressive thickness intrastromal corneal ring segments (PT-ICRS, Keraring AS, Mediphacos, Belo Horizonte, Brazil), and to demonstrate improved visual acuity and symmetry in corneal flattening. Methods: This single-center, retrospective, observational study evaluated the clinical outcomes at 1, 3, and 6 months after implantation of PT-ICRS in patients with duck phenotype keratoconus. After creating the intrastromal tunnel with a femtosecond laser, one 160-degree arc length PT-ICRS, either 150/250 µm or 200/300 µm, was implanted. Changes in uncorrected distance visual acuity (UDVA), corrected distance visual acuity (CDVA), manifest refraction (MR), manifest refraction spherical equivalent (MRSE), mean keratometry (Kmean), maximum keratometry (Kmax), Coma@5mm, and manifest and topographical astigmatism were documented. Results: The study cohort included 23 eyes of 17 patients with a mean age of 24.6 years. From baseline to 6 months following implantation, mean UDVA improved from 0.70 logarithm of the minimum angle of resolution (logMAR) (20/100 Snellen) to 0.22 logMAR (20/33 Snellen), CDVA improved from 0.33 logMAR (20/42 Snellen) to 0.14 logMAR (20/27 Snellen), the mean sphere and MRSE decreased from −1.05 diopters (D) and −2.70 D to −0.25 D and −0.80 D, respectively, and the Kmean and Kmax improved from 46.5 D and 53.7 D to 44.6 D and 48.7 D, respectively. Conclusions: The Keraring AS ICRS offers a safe, effective means of improving visual acuity while reducing refractive error, mean and max keratometry, and aberrations in patients with duck phenotype keratoconus.
Anatomic, computed tomographic, and ultrasonographic assessment of the lymph nodes in presumed healthy adult cats: The head, neck, thorax, and forelimb

Assessment of the lymph nodes is key in staging cancer patients. Descriptions of normal features of the feline lymph nodes using computed tomography (CT) and ultrasound (US) are limited. A prospective anatomic and comparative imaging study was performed. The frequency of identification and the size of the lymph nodes during gross pathology from 6 feline cadavers were compared to the images of lymph nodes from 30 presumed healthy adult cats obtained by CT and US. Measurements (length, width, and height) were compared among techniques. The CT and US features of the identified lymph nodes were also recorded. The frequency of identification of the lymph centers varied among techniques and individually. The mandibular lymph nodes were identified in 100% of the cadavers and in 100% of the healthy cats using CT and US. The medial retropharyngeal lymph nodes were identified in 100% of the cats using CT and US. The deep cervical lymph nodes were not visualized in the cadavers. The cranial mediastinal and tracheobronchial lymph nodes were not visualized using US. Lymph nodes showed a higher length on CT and higher width on US. The height was the most statistically significant variable measurement among techniques. On CT, lymph nodes were most frequently isoattenuating or slightly hypoattenuating to surrounding musculature, with homogeneous contrast enhancement. On US, most lymph nodes were isoechoic or hypoechoic to surrounding fat tissue. The lymph nodes were most frequently elongated or rounded.
Associating executive dysfunction with behavioral and socioemotional problems in children with epilepsy. A systematic review

ABSTRACT As children with epilepsy may have a number of learning and behavioral problems, it is important that insight into the underlying neurocognitive differences in these children, which may underlie these areas of challenge is gained. Executive function (EF) problems particularly are associated with specific learning abilities as well as behavioral problems. We aim to review systematically the current status of empirical studies on the association between EF problems and behavior and socioemotional problems in children with epilepsy. After search, 26 empirical studies were identified, most of them of moderate quality. Overall, attention problems were the most reported cognitive deficit in test assessment and the most reported problem by parents. In 54% of the studies, children with epilepsy scored below average compared to controls/normative samples on different aspects of EF. Most studies reported behavior problems, which ranged from mild to severe. Forty-two percent of the studies specifically reported relationships between EF deficits and behavioral problems. In the remaining studies, below average neuropsychological functioning seemed to be accompanied by above average reported behavioral problems. The association was most pronounced for cognitive control and attention in relation to externalizing behavior problems. This cognitive control is also associated with social functioning. Relevant epilepsy variables in this relationship were early age at onset and high seizure frequency. Future research should distinguish specific aspects of EF and take age into account, as this provides more insight on the association between EF and behavior in pediatric epilepsy, which makes it possible to develop appropriate and early intervention.
Shared genetic architecture across psychiatric disorders

Abstract Psychiatric disorders overlap substantially at the genetic level, with family-based methods long pointing toward transdiagnostic risk pathways. Psychiatric genomics has progressed rapidly in the last decade, shedding light on the biological makeup of cross-disorder risk at multiple levels of analysis. Over a hundred genetic variants have been identified that affect multiple disorders, with many more to be uncovered as sample sizes continue to grow. Cross-disorder mechanistic studies build on these findings to cluster transdiagnostic variants into meaningful categories, including in what tissues or when in development these variants are expressed. At the upper-most level, methods have been developed to estimate the overall shared genetic signal across pairs of traits (i.e. single-nucleotide polymorphism-based genetic correlations) and subsequently model these relationships to identify overarching, genomic risk factors. These factors can subsequently be associated with external traits (e.g. functional imaging phenotypes) to begin to understand the makeup of these transdiagnostic risk factors. As psychiatric genomic efforts continue to expand, we can begin to gain even greater insight by including more fine-grained phenotypes (i.e. symptom-level data) and explicitly considering the environment. The culmination of these efforts will help to inform bottom-up revisions of our current nosology.
Endoscopic management of ampullary tumors: European Society of Gastrointestinal Endoscopy (ESGE) Guideline

Main Recommendations 1 ESGE recommends against diagnostic/therapeutic papillectomy when adenoma is not proven. Strong recommendation, low quality evidence. 2 ESGE recommends endoscopic ultrasound and abdominal magnetic resonance cholangiopancreatography (MRCP) for staging of ampullary tumors. Strong recommendation, low quality evidence. 3 ESGE recommends endoscopic papillectomy in patients with ampullary adenoma without intraductal extension, because of good results regarding outcome (technical and clinical success, morbidity, and recurrence). Strong recommendation, moderate quality evidence. 4 ESGE recommends en bloc resection of ampullary adenomas up to 20–30 mm in diameter to achieve R0 resection, for optimizing the complete resection rate, providing optimal histopathology, and reduction of the recurrence rate after endoscopic papillectomy. Strong recommendation, low quality evidence. 5 ESGE suggests considering surgical treatment of ampullary adenomas when endoscopic resection is not feasible for technical reasons (e. g. diverticulum, size > 4 cm), and in the case of intraductal involvement (of > 20 mm). Surveillance thereafter is still mandatory. Weak recommendation, low quality evidence. 6 ESGE recommends direct snare resection without submucosal injection for endoscopic papillectomy.Strong recommendation, moderate quality evidence. 7 ESGE recommends prophylactic pancreatic duct stenting to reduce the risk of pancreatitis after endoscopic papillectomy. Strong recommendation, moderate quality evidence. 8 ESGE recommends long-term monitoring of patients after endoscopic papillectomy or surgical ampullectomy, based on duodenoscopy with biopsies of the scar and of any abnormal area, within the first 3 months, at 6 and 12 months, and thereafter yearly for at least 5 years. Strong recommendation, low quality evidence.
Physical diseases and elderly suicide in rural China: A case–control psychological autopsy study

Objectives: Physical diseases are well-established risk factor for suicide, particularly among older adults. However, little is known about the underlying mechanism of the association. This study aimed to describe the prevalence of physical diseases and their influences on the elderly in rural China and to examine the underlying mechanisms of the relationship between physical diseases and suicide. Methods: This matched case–control psychological autopsy study was conducted from June 2014 to September 2015. Consecutive suicide cases (242) among people aged 60 years or above were identified in three Chinese provinces. The suicide cases were 1:1 matched with living comparisons based on age, gender and residential area. Two informants for each participant were interviewed to collect data on their demographic characteristics, the severity index of physical diseases, depressive symptoms, feelings of hopelessness, mental disorders and social support. Results: A significant difference was found between suicide cases and living comparisons regarding the prevalence of physical diseases (83.5% vs 66.5%, p < 0.001) and their severity (11.3 ± 6.2 vs 6.7 ± 5.3, p < 0.001). Independent risks of suicide included the following: not currently married (OR = 2.81, 95% CI = [1.04, 7.62]), mental disorders (OR = 7.18, 95% CI = [1.83, 28.13]), depressive symptoms (OR = 1.15, 95% CI = [1.05, 1.26]) and feelings of hopelessness (OR = 1.51, 95% CI = [1.20, 1.90]). The structural equation model indicated that the relationship between the severity index of physical diseases and suicide was mediated by depressive symptoms, feelings of hopelessness and mental disorders. Conclusion: The severity and number of physical diseases were found to be correlated with suicide among the elderly in rural China, after controlling for demographic characteristics. Physical diseases elevate one’s suicide risk by increasing depressive symptoms, feelings of hopelessness and mental disorders. Efforts for suicide prevention should be integrated with strategies to treat physical diseases along with psychological interventions.
Inflammation, depression, and anxiety related to recognition memory in young adults

Abstract Previous research suggests that common modifiable health risk factors (e.g., depression, anxiety, metabolic illness, inflammation) may have an impact on memory. In the present study, we sought to investigate relationships between a number of these health risk factors and two components of recognition memory (recollection and familiarity). Data were analyzed for 96 healthy young adults between 17 and 25 years old. Recollection and familiarity were measured using an associative recognition procedure involving unitized and unrelated word pairs, and regression analyses were used to relate recognition memory performance to physical health (inflammation via plasma IL-6 levels, central obesity via waste-to-hip ratio, and heart rate variability) and mental health (depression via CESD-R, stress via PSS, and state and personality trait anxiety via STAI) measures of modifiable risk factors. Together, these health variables predicted an additional 19% of the variance in recollection beyond what was accounted for by familiarity, and 15% of the variance in familiarity beyond what was accounted for by recollection. These effects were primarily driven by inflammation, depression, and trait anxiety, which were each significant (p < .05) independent predictors of recognition. Higher levels of depression and inflammation were related to worse recollection yet better familiarity. Higher levels of trait anxiety were related to better recollection but were not related to familiarity. These findings demonstrate complex relationships between these modifiable health risk factors and recognition memory. Future longitudinal and cross-sectional research is needed to further explore these relationships and determine whether or not poor health causes these changes in recognition.
Locoregional options in the management of cholangiocarcinoma: single center experience.

BACKGROUND The purpose of this case series is to assess the safety and efficacy, as well as the overall survival (OS) and progression free survival (PFS) of patients with intrahepatic cholangiocarcinoma (ICC) treated with percutaneous ablation, transarterial arterial chemoembolization (TACE) or a combination of both at our institution. METHODS Ten patients with pathological diagnosis of adenocarcinoma treated at out institution between January 1st 2013 and January 1st 2019 were reviewed. Three patients received a combined TACE and ablation treatment, three patients received TACE without ablation and four patients were treated with ablation only. Ablation technical success was determined by absence of residual tumor in the ablation zone on follow-up imaging one-month post-ablation. TACE response was assessed using the Modified Response Evaluation Criteria in Solid Tumors (mRECIST). Technical success was defined as injection of chemoembolic material in the involved liver lobes. PFS and OS were calculated from the date of diagnosis. RESULTS In the TACE and radiofrequency ablation (RFA) group, OS was 12, 55 and 56 months; PFS was 5, 6 and 32 months, one patient died and two others remain alive. In the TACE group, OS was 29, 10 and 5 months; PFS was 15, 10 and 4 months. All three patients remain alive. In the ablation group, OS and PFS were 16, 31, 30 and 40 months. All patients remain alive. Overall, 9 of 10 patients are alive, with a Median OS and PFS of 29.5 and 15.5 months, respectively, with some patients remain alive over four years following initial presentation. CONCLUSIONS Our study shows that ablation and TACE in combination with more traditional modalities such as chemoradiation and surgical resection can extend survival in patients with ICC significantly. Locoregional therapy is well tolerated with only minor adverse events. The use of stereotactic body radiation therapy (SBRT) with ablation demonstrated the synergistic nature of using multiple lines of interventions.
Breast cancer rate after oophorectomy: A Prospective Danish Cohort Study

The association between oophorectomy and risk of breast cancer in the general population is uncertain. The aim of our study was to determine the breast cancer rate in women from the general population after oophorectomy (performed before/after menopause), and whether this varies by use of hormone replacement therapy (HRT), hysterectomy, body mass index (BMI) and shift work. The study included 24 409 female nurses (aged ≥45 years) participating in the Danish Nurse Cohort. Nurses were followed from cohort entry until date of breast cancer, death, emigration or end of follow‐up at 31 December 2018, whichever came first. Poisson regression with log‐transformed person‐years as the offset examined the association between oophorectomy and breast cancer (all ages and stratified by menopausal status at time of oophorectomy). The potential modifying effect of HRT use, hysterectomy, BMI and shift work on the associations was estimated. During 502 463 person‐years of follow‐up, 1975 (8.1%) nurses were diagnosed with breast cancer. Bilateral oophorectomy was associated with a reduced breast cancer rate compared to nurses with preserved ovaries, adjusted rate ratio (95% confidence interval): 0.79 (0.64; 0.99). Similar associations (magnitude and direction) were detected for unilateral oophorectomy and when stratifying according to menopausal status at time of oophorectomy, but without statistical significance. Unilateral and bilateral oophorectomy is associated with a reduced breast cancer rate in women from the general population. This association is not modified by use of HRT, hysterectomy, BMI or shift work.