Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Respiratory Tract Microbiome Between Carbapenem-Resistant Acinetobacter baumannii Colonization and Ventilator Associated Pneumonia

Background Carbapenem-resistant Acinetobacter baumannii (CRAB) is a common cause of ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients, but its infection and colonization state are difficult to distinguish. If the judgment is wrong, it may aggravate the abuse of antibiotics and further accelerate the evolution of drug resistance. We sought to provide new clues for the diagnosis, pathogenesis and treatment of CRAB VAP based on lower respiratory tract (LRT) microbiota. Methods A prospective study was conducted on patients with mechanical ventilation from July 2018 to December 2019 in a tertiary hospital. Multi-genomics studies (16S rRNA amplicon, metagenomics, and whole-genome sequencing [WGS]) of endotracheal deep aspirate (ETA) were performed. Results Fifty-two ICU patients were enrolled, including 24 with CRAB VAP (CRAB-I), 22 with CRAB colonization (CRAB-C), and six CRAB-negative patients (infection-free) (CRAB-N). Diversity of pulmonary microbiota was significantly lower in CRAB-I than in CRAB-C or CRAB-N (mean Shannon index, 1.79 vs. 2.73 vs. 4.81, P < 0.05). Abundances of 11 key genera differed between the groups. Acinetobacter was most abundant in CRAB-I (76.19%), moderately abundant in CRAB-C (59.14%), and least abundant in CRAB-N (11.25%), but its interactions with other genera increased in turn. Metagenomics and WGS analysis showed that virulence genes were more abundant in CRAB-I than in CRAB-C. Multi-locus sequence typing (MLST) of 46 CRAB isolates revealed that the main types were ST208 (30.43%) and ST938 (15.22%), with no difference between CRAB-I and CRAB-C. Conclusion Lower respiratory tract microbiota dysbiosis including elevated relative abundance of Acinetobacter and reduced bacterial interactions, and virulence enrichment may lead to CRAB VAP.
Titles and Semantic Violations Affect Eye Movements When Viewing Contemporary Paintings

The role of titles in perception of visual art is a topic of interesting discussions that brings together artists, curators, and researchers. Titles provide contextual cues and guide perception. They can be particularly useful when paintings include semantic violations that make them challenging for viewers, especially viewers lacking expert knowledge. The aim of this study is to investigate the effects of titles and semantic violations on eye movements. A total of 127 participants without expertise in visual art viewed 40 paintings with and without semantic violations (20 each) in one of three conditions: untitled, consistent titles and inconsistent titles. After each painting was viewed participants also rated liking and understanding. Our results suggest that titles affect the way paintings are viewed: both titled conditions were associated with shorter first fixation duration, longer saccade durations, and amplitudes and higher dynamic entropy than the untitled conditions. Titles were fixated on more frequently (but only in the time window between 1,200 and 2,800 ms) when presented alongside paintings with semantic violations than paintings without violations, and the percentage of fixations to titles was particularly high in the case of paintings with double inconsistencies (inconsistent titles and semantic violations). Also, we found that semantic violations attracted attention early on (300–900 ms), whereas titles received attention later (average first fixation on title was at 936.28 ms) and inconsistencies in titles were processed even later (after 4,000 ms). Finally, semantic violations were associated with higher dynamic entropy than paintings without violations. Our results demonstrate the importance of titles for processing of artworks, especially artworks that present a challenge for the viewers.
Fatty Acids, Amphiregulin Production, and Lung Function in a Cohort of Midwestern Veterans

Rationale The relationship between many fatty acids and respiratory outcomes remains unclear, especially with regard to mechanistic actions. Altered regulation of the process of lung repair is a key feature of chronic lung disease and may impact the potential for pulmonary rehabilitation, but underlying mechanisms of lung repair following injury or inflammation are not well-studied. The epidermal growth factor receptor agonist amphiregulin (AREG) has been demonstrated to promote lung repair following occupational dust exposure in animals. Studies suggest the polyunsaturated fatty acid (PUFA) docosahexaenoic acid (DHA) may enhance the production of AREG. The objective of this study was to determine the relationship between fatty acids and lung function in a population of veterans and determine if fatty acid status is associated with concentrations of AREG. Materials and Methods Data were collected from a cross-sectional study of veterans within the Nebraska-Western Iowa Health Care System. Whole blood assays were performed to quantify AREG concentrations via a commercially available ELISA kit. Fatty acids from plasma samples from the same patients were measured using gas-liquid chromatography. Intakes of fatty acids were quantified with a validated food frequency questionnaire. Linear regression models were used to determine whether plasma fatty acids or intakes of fatty acids predicted lung function or AREG concentrations. A p < 0.05 was considered statistically significant. Results Ninety participants were included in this analysis. In fully adjusted models, plasma fatty acids were associated with AREG production, including the PUFA eicosapentaenoic acid (EPA) (β = 0.33, p = 0.03) and the monounsaturated fatty acid octadecenoic acid: (β = −0.56, p = 0.02). The omega-3 PUFA docosapentaenoic acid (DPA) was positively associated with lung function (β = 0.28, p = 0.01; β = 26.5, p = 0.05 for FEV1/FVC ratio and FEV1 % predicted, respectively), as were the omega-6 PUFAs eicosadienoic acid (β = 1.13, p < 0.001; β = 91.2, p = 0.005 for FEV1/FVC ratio and FEV1 % predicted, respectively) and docosadienoic acid (β = 0.29, p = 0.01 for FEV1/FVC ratio). Plasma monounsaturated and saturated fatty acids were inversely associated with lung function. Conclusion Opposing anti- and pro-inflammatory properties of different fatty acids may be associated with lung function in this population, in part by regulating AREG induction.
Simulation-Assisted Determination of the Minimum Melting Temperature Composition of MgCl2–KCl–NaCl Salt Mixture for Next-Generation Molten Salt Thermal Energy Storage

Molten chloride mixtures such as MgCl2–KCl–NaCl are potential thermal energy storage (TES) materials and heat transfer fluids (HTFs) for next-generation concentrating solar power (CSP) systems due to their high operation temperatures (>700°C) and low costs. This ternary MgCl2–KCl–NaCl salt mixture with a low material cost (<0.35 $/kg) is a promising salt for high-temperature TES/HTF applications, for example, it could enable next-generation CSP plants to have significant power cycle efficiency and lower levelized cost of electricity (LCOE). In this study, the minimum melting temperature composition for the MgCl2–KCl–NaCl mixture was estimated by FactSage simulation, while the binary and ternary phase diagrams of the MgCl2–KCl–NaCl salt system, including their phase transitions, were studied. Five different eutectic compositions of the MgCl2–KCl–NaCl mixture from literature and simulations were selected to determine the minimum melting temperature composition by the differential scanning calorimetry technique. Results show agreement between experiments and simulations of the melting temperature and its composition. Hence, values of the exact and reliable minimum melting temperature and salt composition in mol% and wt% are given. Based on the determined melting temperature, the minimum operating temperature of MgCl2–KCl–NaCl is recommended according to the safety margin for CSP applications.
Associations Between the Macular Microvasculatures and Subclinical Atherosclerosis in Patients With Type 2 Diabetes: An Optical Coherence Tomography Angiography Study

Objective To investigate the associations between the macular microvasculature assessed by optical coherence tomography angiography (OCTA) and subclinical atherosclerosis in patients with type 2 diabetes. Methods We included patients with type 2 diabetes who received comprehensive medical and ophthalmic evaluations, such as carotid ultrasonography and OCTA at a hospital-based diabetic clinic in a consecutive manner. Among them, 254 eyes with neither diabetic macular edema (DME) nor history of ophthalmic treatment from 254 patients were included. The presence of increased carotid intima-media thickness (IMT) (>1.0 mm) or carotid plaque was defined as subclinical atherosclerosis. OCTA characteristics focused on foveal avascular zone (FAZ) related parameters and parafoveal vessel density (VD) were compared in terms of subclinical atherosclerosis, and risk factors for subclinical atherosclerosis were identified using a multivariate logistic regression analysis. Results Subclinical atherosclerosis was observed in 148 patients (58.3%). The subclinical atherosclerosis group were older (p < 0.001), had a greater portion of patients who were men (p = 0.001) and who had hypertension (p = 0.042), had longer diabetes duration (p = 0.014), and lower VD around FAZ (p = 0.010), and parafoveal VD (all p < 0.05). In the multivariate logistic regression analysis, older age (p ≤ 0.001), male sex (p ≤ 0.001), lower VD around FAZ (p = 0.043), lower parafoveal VD of both superficial capillary plexus (SCP) (p = 0.011), and deep capillary plexus (DCP) (p = 0.046) were significant factors for subclinical atherosclerosis. Conclusion The decrease in VD around FAZ, and the VD loss in parafoveal area of both SCP and DCP were significantly associated with subclinical atherosclerosis in patients with type 2 diabetes, suggesting that common pathogenic mechanisms might predispose to diabetic micro- and macrovascular complications.
Association Between Dietary Fluoride and Calcium Intake of School-Age Children With Symptoms of Dental and Skeletal Fluorosis in Halaba, Southern Ethiopia

Background In the Ethiopian Rift Valley, ways to reduce the fluoride (F) burden from drinking water have been unsuccessful. Calcium (Ca) intake may mitigate fluorosis by binding with F ions and preventing absorption. The purpose of this study was to examine the association between Ca intake and proportion of fluorosis symptoms in school-age children in an area where F levels are known to be higher than WHO limit of 1.5 mg F/L water. Methods A cross-sectional survey in the Halaba zone involved 135 eligible children aged 6–13 year who were recruited to have dental fluorosis assessed by a dentist and skeletal fluorosis assessed by a physiotherapist. Dietary Ca intake was determined by 24-h recall. Food items and samples from ground wells, taps and spring water were collected for F concentration. Associations were measured using bivariate logistic regression, adjusted for known confounders. Results Water F averaged 5.09 mg/L. Total F intake was high, 10.57 mg/day, and Ca intake was low, 520 mg/day. Prevalence of dental fluorosis (from very mild to severe symptoms) was 73.1% for younger children (6–8 years) and 68.3 % for older children (9–13 years). The prevalence of children having symptoms of skeletal fluorosis ranged between 55.1 and 72.4%, with no apparent age difference. Dietary F intake of children was significantly positively associated with presence of dental fluorosis. Dietary Ca intake of children was significantly negatively associated with dental fluorosis. Higher than average dietary F intake significantly increased the odds of developing skeletal fluorosis symptoms when measured as inability to stretch and fold arms to touch back of head. Higher than average Ca intake was significantly associated with decreased odds of developing skeletal fluorosis measured as inability to bend body to touch the toes or floor. Conclusions High dietary F, as expected, was associated with fluorosis in children. In the presence of higher Ca intake (>520 mg/day) some fluorosis symptoms were mitigated. There is a need to improve Ca intakes as all were below recommended levels, and this nutritional strategy may also reduce burden of excess F.
Recurrent Severe Subclinical Mastitis and the Risk of HIV Transmission Through Breastfeeding

Subclinical mastitis (SCM) is an important risk factor of postnatal HIV-1 transmission that is still poorly understood. A longitudinal sub-study of the ANRS12174 trial including 270 breastfeeding mothers in Lusaka, Zambia measured sodium (Na+) and potassium (K+) in archived paired breast milk samples collected at week 14, 26 and 38 postpartum to determine cumulative incidence of SCM and the effects of recurrent severe SCM on HIV-1 shedding in breast milk. A nested retrospective cohort study including 112 mothers was also done to determine longitudinal effects of SCM on four pro-inflammatory cytokines; IL6, IL8, IP10 and RANTES. The cumulative incidence for any SCM (Na+/K+ ratio > 0.6) and severe SCM (Na+/K+ ratio > 1) were 58.6% (95%CI: 52.7 – 64.5) and 27.8% (95%CI: 22.5 – 33.1), respectively. In majority of affected mothers (51.4%) severe SCM was recurrent. Both breasts were involved in 11.1%, 33.3% and 70% of the mothers with a single episode, 2 and 3 episodes respectively. In affected breasts, an episode of severe SCM resulted in steep upregulation of the four cytokines considered (IL8, IP10, RANTES and IL6) compared to: before and after the episode; contralateral unaffected breasts; and SCM negative control mothers. Recurrent severe SCM significantly increased the odds of shedding cell-free HIV-1 in breast milk (OR: 5.2; 95%CI: 1.7 – 15.6) whereas single episode of severe SCM did not (OR: 1.8; 95%CI: 0.8 – 4.2). A Na+/K+ ratio > 1 indicative of severe SCM is an excellent indicator of breast inflammation characterized by a steep, localized and temporal upregulation of several pro-inflammatory cytokines that favor HIV-1 shedding in mature breast milk and may facilitate postnatal HIV-1 transmission through breastfeeding.
Cervical Cancer Recurrence and Patient Survival After Radical Hysterectomy Followed by Either Adjuvant Chemotherapy or Adjuvant Radiotherapy With Optional Concurrent Chemotherapy: A Systematic Review and Meta-Analysis

Objective To compare cervical cancer recurrence and patient survival after radical hysterectomy followed by either adjuvant chemotherapy (AC) or adjuvant radiotherapy with or without concurrent chemotherapy (AR/CCRT). Methods We systematically searched PubMed, EMBASE, the Cochrane Library and clinicaltrials.gov to identify studies reporting recurrence or survival of cervical cancer patients who received AC or AR/CCRT after radical hysterectomy. Data were meta-analyzed using a random-effects model, and heterogeneity was evaluated using the I2 test. Subgroup and sensitivity analyses were performed to identify potential sources of heterogeneity. Results The meta-analysis included 14 non-randomized studies and two randomized controlled trials, altogether involving 5,052 cervical cancer patients. AC and AR/CCRT groups did not differ significantly in rates of total or local recurrence or mortality. Nevertheless, AC was associated with significantly lower risk of distant recurrence [odds ratio (OR) 0.67, 95% confidence interval (CI) 0.55-0.81] and higher rates of overall survival [hazard ratio (HR) 0.69, 95%CI 0.54-0.85] and disease-free survival rate (HR 0.77, 95%CI 0.62-0.92). Conclusions AC may be an effective alternative to AR/CCRT for cervical cancer patients after radical hysterectomy, especially younger women who wish to preserve their ovaries and protect them from radiation damage. Systematic Review Registration https://www.crd. york.ac. uk/prospero/, identifier PROSPERO (CRD42021252518).
How Is Mass Spectrometry Tackling the COVID-19 Pandemic?

Most of us have never faced a pandemic before. The World Health Organization declared the 2019 novel coronavirus infectious disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 virus), a pandemic by March 11th, 2020. Today, this illness has reported more than 5′331,019 fatalities worldwide (December 17th, 2021). The COVID-19 pandemic has posed an unprecedented global challenge and put the academic community on “the spot. ” The following mini-review reports how the MS community improved the understanding of the SARS-CoV-2 virus pathophysiology while developing diagnostic procedures to complement the PCR-based approaches. For example, MS researchers identified the interaction sites between the SARS-CoV-2 virus and their hosts; this new knowledge is critical for developing antiviral drugs. MS researchers also realized that COVID-19 should be considered a systemic disease and not just a respiratory illness since its metabolic, lipidomic, and proteomic profile reflects four different clinical disorders: 1) acute inflammatory response, 2) a cardiovascular disease, 3) a prediabetic/diabetes and 4) liver dysfunction. Furthermore, MS researchers put forth the knowledge that the metabolic and lipidomic profile of several patients remained altered after being discharged, thus hinting at the scientific basis for the long COVID syndrome.
A Multi-Factor Approach to the Study of L2 Acquisition of Motion Verbs and Motion Constructions: Integration of Typological, Psycholinguistic and Sociolinguistic Aspects

Talking about motion events in L2 is done in different ways by different speakers on different occasions. This is due to multiple factors, typological, psycholinguistic and sociolinguistic, which interact and play a role in L2 acquisition and use. These factors can sometimes lead the same types of L2 speakers to produce very different outputs and sometimes very different L2 speakers to produce the same or similar outputs. In order to capture this diversity of outcomes the CASP (Complex Adaptive System Principles) for Bilingualism model was proposed and we illustrate how this model helps us formulate predictions about motion event verbalizations, set up experiments and account for results in a holistic manner, taking into consideration the relevant multiple factors. Furthermore, a lot of effort in the field has gone into contrasting monolingual and bilingual populations while more knowledge is needed about how different bilingual populations compare. These different bilinguals, including L2 learners, need to be tested under different conditions in which they use their languages (e.g., when only one or both is actively used with vs. without the possibility to code-switch) in order to understand the variability of L2 verbal behaviours and the underlying factors at play under different circumstances of acquisition and use. This perspective paper provides both theoretical and empirical indications how this can be done, with the key message that future research into L2 acquisition (and bilingualism in general) must be based on a multi-factor approach.
An Ultrasonic-Based Radiomics Nomogram for Distinguishing Between Benign and Malignant Solid Renal Masses

Objectives This study was conducted in order to develop and validate an ultrasonic-based radiomics nomogram for diagnosing solid renal masses. Methods Six hundred renal solid masses with benign renal lesions (n = 204) and malignant renal tumors (n = 396) were divided into a training set (n = 480) and a validation set (n = 120). Radiomics features were extracted from ultrasound (US) images preoperatively and then a radiomics score (RadScore) was calculated. By integrating the RadScore and independent clinical factors, a radiomics nomogram was constructed. The diagnostic performance of junior physician, senior physician, RadScore, and radiomics nomogram in identifying benign from malignant solid renal masses was evaluated based on the area under the receiver operating characteristic curve (ROC) in both the training and validation sets. The clinical usefulness of the nomogram was assessed using decision curve analysis (DCA). Results The radiomics signature model showed satisfactory discrimination in the training set [area under the ROC (AUC), 0.887; 95% confidence interval (CI), 0.860–0.915] and the validation set (AUC, 0.874; 95% CI, 0.816–0.932). The radiomics nomogram also demonstrated good calibration and discrimination in the training set (AUC, 0.911; 95% CI, 0.886–0.936) and the validation set (AUC, 0.861; 95% CI, 0.802–0.921). In addition, the radiomics nomogram model showed higher accuracy in discriminating benign and malignant renal masses compared with the evaluations by junior physician (DeLong p = 0.004), and the model also showed significantly higher specificity than the senior and junior physicians (0.93 vs. 0.57 vs. 0.46). Conclusions The ultrasonic-based radiomics nomogram shows favorable predictive efficacy in differentiating solid renal masses.
Microtubule Motor Transport of Organelles in a Specialized Epithelium: The RPE

The retinal pigment epithelium (RPE) is a uniquely polarized epithelium that lies adjacent to the photoreceptor cells in the retina, and is essential for photoreceptor function and viability. Two major motile organelles present in the RPE are the melanosomes, which are important for absorbing stray light, and phagosomes that result from the phagocytosis of the distal tips of the photoreceptor cilium, known as the photoreceptor outer segment (POS). These organelles are transported along microtubules, aligned with the apical-basal axis of the RPE. Although they undergo a directional migration, the organelles exhibit bidirectional movements, indicating both kinesin and dynein motor function in their transport. Apical melanosome localization requires dynein; it has been suggested that kinesin contribution might be complex with the involvement of more than one type of kinesin. POS phagosomes undergo bidirectional movements; roles of both plus- and minus-end directed motors appear to be important in the efficient degradation of phagosomes. This function is directly related to retinal health, with defects in motor proteins, or in the association of the phagosomes with the motors, resulting in retinal degenerative pathologies.