Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic profiles of Pseudomonas aeruginosa gene clusters based on profile HMMs, reveal novel therapeutic targets for clinical intervention

Pseudomonas aeruginosa has developed antibiotic resistance, a major health concern worldwide, through different mechanisms including the formation of biofilms. Thus far, typing has been primarily assay based. However, the many sequences available from the US National Center for Biotechnology Information (NCBI) and the International Consortium of Pseudomonas Database (IPCD) offer alternative ways of characterizing the biofilm formation genes which would reveal novel therapeutic targets for intervention. The current study employed profile hidden Markov models (pHMMs) in the characterization of biofilm formation genes and identification of possible variations based on the different ecological niches occupied by strains of P. aeruginosa. Statistical analyses were performed in R (v. 3.1.3) to determine the significance of these variations. Validated pHMMs identified a total of 197 hits for the 13 different ecological niches, with the human metagenomes recording 144 hits (73%) while the non-human metagenomes recorded 53 hits (27%). Human metagenomes had a significantly higher density of hits, with the abscess metagenomes indicating the highest density of hits. The overall result indicated a significant variation in density of hits between the different sites within the human metagenomes. This study successfully highlighted the significant value of already sequenced metagenomes in the identification of potential targets for novel therapeutic compounds. The profile hidden Markov model successfully identified 197 unique biofilm gene clusters emphasizing its importance in analyzing different sequenced pathogenic strains. The study recommends that experimental assays could be carried out to shed further light on the different biofilm formation gene clusters. Key words: Profile hidden Markov model, metagenomics, biofilm formation, antibiotic resistance.
Novel solid-state heavy rare-earth (III) picolinates: A pyrolytic study using: TG- DSC-FTIR, HSM-MS and GC-MS

Heavy trivalent lanthanides and yttrium picolinates were synthesized by complexation of basic rare-earth metal carbonates with an aqueous solution of picolinic acid. The novel compounds were obtained with the general formula Ln(L)3∙nH2O, where L is picolinate and n= 1.5 H2O (Dy, Ho, Yb, Lu and Y), 2 H2O (Tb and Tm) and 2.5 H2O (Er). The stoichiometry of the complexes was calculated through mass losses found using thermogravimetry (TG), complexometry and elemental analysis (EA). The thermal behavior in oxidative and pyrolytic atmospheres of the compounds was analyzed by simultaneous thermogravimetry differential scanning calorimetry (TG-DSC). The gaseous products of the pyrolysis were determined throughout by monitoring the evolved species using TG-DSC, Fourier transform infrared spectroscopy (TG-DSC-FTIR), hot-stage microscopy mass spectrometry (HSM-MS), and gas chromatography-mass spectrometry (GCMS). The obtained results validated mass loss assignments made using the TG curves. However, gaseous product analysis indicates the degradation processes are more complex than the thermoanalytical techniques suggest alone. This study used a GC-MS technique to identify the condensed gaseous products obtained during the second step of the thermal degradation of the picolinate complexes. The analysis of the symmetric and asymmetric stretching frequencies of the carboxylate group in the FTIR spectra showed a monodentate bonding mode. The compounds were obtained in the amorphous state, as indicated by the powder X-ray diffractometry (PXRD) data. Keys works: Heavy trivalent lanthanide picolinates, evolved gas analysis (EGA), TG-DSC-FTIR, HSM-MS, GC-MS. 1 Corresponding author. e-mail address: nascimento.a. l.c@gmail.com
Prognostic Nutritional Index identifies risk of early progression and survival outcomes in Advanced Non-small Cell Lung Cancer patients treated with PD-1 inhibitors

Background: The prognostic nutritional index (PNI) is related to the prognosis of multiple malignancies. This study investigated whether the PNI has prognostic value in advanced non-small cell lung cancer (NSCLC) patients treated with programmed death 1 (PD-1) inhibitors. Methods: We retrospectively analyzed advanced NSCLC patients treated with PD-1 inhibitors from July 2018 to December 2019. Pretreatment PNI was calculated by peripheral lymphocyte count and serum albumin level, and the cut-off value was determined. Subsequently, we investigated the relationship between PNI and early progression, and evaluated its prognostic role on survival outcomes. Ultimately, based on the results of survival analysis, a nomogram was established. Results: A total of 123 patients were included. Of these, 24 (19.5%) patients had experienced early progression. Multivariate logistic analysis indicated that low PNI (odds ratio, 3.709, 95% confidence interval [CI], 1.354-10.161; P = 0.011) was closely correlated with early progression. Moreover, multivariate Cox regression analysis confirmed that low PNI was an independent risk factor for progression-free survival (hazard ratio [HR], 2.698, 95% CI, 1.752-4.153; P < 0.001) and overall survival (HR, 7.222, 95% CI, 4.081-12.781; P < 0.001), respectively. The prediction accuracy of nomogram based on PNI is moderate. Conclusion: PNI was an independent predictor of early progression and survival outcomes in advanced NSCLC patients treated with PD-1 inhibitors.
Preservice Teachers’ Sense of Belonging During Practicum Placements

Practicum placements in schools are keystone features of preservice teacher education, yet inconsistencies in their nature and quality are pervasive. This phenomenon was explored in two cultural contexts, with a focus on ‘belonging’, which the literature reveals may impact practicums and commitment to the profession. Interviews were conducted with six primary school preservice teachers in Australia and Scotland, about their lived experience of belonging/non-belonging during practicum. Hermeneutic phenomenological analysis revealed four themes in both cultural contexts: 1. Being welcomed; 2. Settings and procedures; 3. Interpersonal interactions; and, 4. Strategic behaviours. This study indicates belonging as crucial to preservice teachers’ cognition, wellbeing and learning during practicums, with ‘non-belonging’ inhibiting their development. Preservice teacher and mentor preparedness for practicums is highlighted, alongside challenges for initial teacher education programs and schools in addressing the fundamental need to foster a sense of belonging for preservice teachers during this crucial aspect of their teacher preparation.
The Production and Consumption of Social Media

We model social media as collections of users producing and consuming content. Users value consuming content but, due to scarce attention, they may not value all content from other users. Users also value receiving attention, creating the incentive to attract an audience by producing valuable content, but also through attention bartering---users mutually becoming each others' audience. Attention bartering shapes substantially the patterns of production and consumption on social media, explains key features of social media behavior and platform decision-making, and yields sharp predictions that are consistent with data we collect from #EconTwitter. The full paper can be accessed online at http://www.apostolos-filippas.com/papers/twitter.pdf.
Evaluation of Aflatoxin-Related Products from Ozonated Corn

This study assessed the efficacy of the ozonation process in degrading aflatoxin in corn, and investigated the chemical reaction between aflatoxin and gaseous ozone. Ozonation (12-13 wt%) totally degraded aflatoxin B1 in a model system. Conversion of aflatoxin into polar compounds was observed during ozonolysis of 100 µg aflatoxin B1 in an aqueous environment and in solid form. Seven intermediate reaction products were separated by two-dimensional thin layer chromatography. HPLC analysis of ozonated AFB1 revealed the presence of six major peaks. MALDI-MS analysis detected compounds that have higher molecular weights than AFB1. The dichloromethane fraction contained compounds with molecular ion peaks at 459 and 439 m/z while the water fraction contained compounds with molecular ion peaks at 475 and 494 m/z, after ozonation for 50 sec and 60 sec, respectively. Biosynthesis of [14-C]-labeled aflatoxin B1 by Aspergillus flavus (A53, C50Aa) and sodium acetate-1,2-[14C] as a precursor yielded 339 µg of [14C]-AFB1 with a specific activity of 1.06 µCi/µmol (7548 dpm/µg). Corn kernels inoculated with Aspergillus flavus (A53, C50Aa) resulted in the production of grains contaminated with aflatoxin B1 (7452 ng/g) and aflatoxin B2 (704 ng/g). Modification of AFB1 after treatment with gaseous ozone was determined using [14C]-labeled AFB1. Ozonated and non-ozonated corn spiked with [14C]-AFB1 were evaluated and compared through a series of extraction, partition, and digestion procedures. Ozonation (9-10 wt%) resulted in 74% and 44% reduction of AFB1 and AFB2 levels, respectively. Radioactivity measured by liquid scintillation counting showed an increase in the percentage of radioactivity in more polar and aqueous solvents from ozonated corn compared with non-ozonated corn. These results suggested the formation of more polar and/or water soluble aflatoxin-related compounds from the reaction of ozone with AFB1. Based on these results, it is postulated that ozone attacked the double bond in the C8-C9 position and converted aflatoxin B1 into an aldehyde.
Assessment of original dental diagnostic program in the opinion of dentists

Introduction: An increase of information, especially in the field of medicine and dentistry, has led to the development of areas related to diagnosis and treatment. Rapid pace of development means that doctors around the world want to practice evidence-based medicine with the latest research results. The condition for successful treatment is the correct diagnosis. Objectives: The aim of the study was to develop a computer algorithm for a dental office and evaluate dentists’ opinions about the computer algorithm created by the author for dental diagnostics. Material and methods: The research was carried out in a group of dentists in a private dentist’s office. Dentists performed treatment according to their well-known standards (group 1), then according to proposed algorithm (group 2), and filled a questionnaire comparing both methods. Results: Algorithm evaluation was performed by dentists on a group of 300 treated patients, with 156 women (52%) and 144 men (48%), and the average age was 34.13 years. For the majority of conducted examinations (88.67, 99%), dentists stated that the algorithm used during an interview and examination fulfilled their expectations. Statistically significantly higher time values needed to conduct medical interview in accordance with the proposed study algorithm were found in men compared to women ( p < 0.05). Conclusions: The application of the proposed diagnostic algorithm was positively received by dental doctors. Most dentists considered working using the algorithm as facilitating the communication with the patient and increasing his participation in the treatment process. The conducted research indicated the need for a holistic approach to the patient, raising awareness of the impact of systemic diseases on the state of oral health.
Enhanced Buffer Gas Loading: Cooling and Trapping of Atoms with Low Effective Magnetic Moments

A new technique for buffer gas loading is described. This technique greatly extends the range of atoms and molecules that may be magnetically trapped at low temperature. The advance is made possible by the rapid removal of the buffer gas on a time scale one hundred times greater than in previous buffer gas loading experiments. A new cryogenic valve is developed and employed. The following benchmarks were attained in our first experimental run; approximately 10 atoms with effective magnetic moments μeff & 3μB were trapped and thermally isolated with near unit efficiency, ~ 10 μeff = 2μB atoms were trapped and thermally isolated, and ~ 10 μeff = 1μB atoms were trapped, but without thermal isolation. For comparison, all previous buffer gas loading experiments that achieved thermal isolation after trapping were done with atoms having a magnetic moment of at least 6μB. In our second run of the experiment, better temperature management allowed us to increase the number of trapped and thermally isolated μeff = 2μB atoms to ~10 and trapped μeff = 1μB atoms to ~ 10. The performance of the present apparatus is limited by the presence of a desorbing helium film that compromises the vacuum in the cell after the bulk of the buffer gas is removed. Future improvements to address this problem are suggested that will likely allow for efficient trapping and thermal isolation of atoms and molecules with magnetic moments as low as 1μB. Analysis of the trapping and pumping dynamics is presented.
Face-to-face Interactions, Tenant Resilience, and Commercial Real Estate Performance

We study the impact of face-to-face (FTF) interactions on commercial real estate (CRE) performance. By linking tenants, properties, and CRE firms, we construct three novel FTF measures that capture tenant remote working, internal communication between coworkers, and external contact with customers. Using the COVID-19 pandemic as an exogenous shock to the FTF economy, we find that firms holding properties with tenants that are more resilient to social distancing perform better. These FTF effects weaken over the long term, however. As investors are capable of compiling valuable information at granular levels regarding how tenants operate, our findings support market efficiency and shed light on postpandemic CRE performance. © 2022 American Real Estate and Urban Economics Association.
The challenge of asymptomatic carriers of COVID-19: A rapid review of literature.

OBJECTIVES To describe the epidemiological and sociodemographic characteristics of asymptomatic carriers reported in the literature, and to review the strategies used for diagnosis and control. METHODS Systematic literature review approach. As inclusion criteria, all studies published between January 1 and June 26, 2020, conducted in humans, that reported people who remained asymptomatic of COVID-19. Descriptors were adapted to the interfaces of eight bibliographic databases were configured: PubMed, Ovid, SciELO, Ebsco, Scopus, LILACS, Epistemonikos and Embase. RESULTS About 45% of the articles reported adult population, thirteen reported mixed population (adult and pediatric). 3 525 asymptomatic people were reported, with an average of 37,1 years [0.5-82 years]. Although the effectiveness of the control and prevention measures was not reported, the identification, isolation and follow-up of contacts stands out as a potential effective mechanism to prevent the transmission. CONCLUSIONS The use of this information could be relevant to guide evidence-based public health policies and the protection of populations and the improvement of health care that contributes to stopping this pandemic.
Return to normal: COVID-19 vaccination under mitigation measures

Being unable to suppress SARS-CoV-2 transmission, the majority of countries worldwide have resorted to a mitigation approach towards COVID-19, allowing some degree of viral circulation in the population. Here, we investigate the expected outcomes of the interplay between vaccination rollout and adaptive mitigation measures constantly altering the epidemic trajectory and keeping the reproduction number around the unit. Using a novel mathematical modeling framework, we estimate that, for vaccination capacities of at least 4 daily doses administered per 1,000 inhabitants, a complete release of mitigation measures can be expected within 7 to 13 months since the start of vaccination, with a two-year cumulative incidence of deaths between 0.18 and 0.46 per 1,000 population. A heavier burden of deaths and a delayed <<return-to-normal>> is expected for lower vaccine capacities, if viral transmissibility exceeds by >60% the one estimated at the beginning of the pandemic, or if vaccine protection is short-lived. Failure to prioritize the elderly or a premature release of mitigation measures after vaccination of the most fragile will conspicuously increase the expected mortality. Finally, strategies oriented to prioritize the suppression of SARS-CoV-2 by maintaining strict restrictions will take a similar time as a mitigation approach, possibly resulting in acceptability issues. Persisting unknowns about the evolving epidemiology of SARS-CoV-2 variants and on the effectiveness of available and upcoming vaccines may warrant a future reassessment of these conclusions.
Improving postpartum hemorrhage risk prediction using longitudinal electronic medical records

Objective: Postpartum hemorrhage (PPH) remains a leading cause of preventable maternal mortality in the US. Our goal was to develop a novel risk assessment tool and compare its accuracy to those used in current practice. Materials and Methods: We used a PPH digital phenotype we developed and validated previously to identify 6,639 cases from our delivery cohort (N=70,948). Using a vast array of known and potential risk factors extracted from electronic medical records available prior to delivery, we trained a gradient boosting model in a subset of our cohort. In a held-out test sample, we compared performance of our model to three clinical risk tools and one previously published model. Results: Our 24-feature model achieved an area under the curve (AUC) of 0.71 (95% confidence interval [CI], 0.69-0.72), higher than all other tools (research-based AUC: 0.67 [95%CI, 0.66-0.69], clinical AUCs: 0.55 [95%CI, 0.54-0.56] to 0.61 [95%CI, 0.59-0.62]). Five features were novel including red blood cell indices and infection markers measured standardly upon admission. Additionally, we identified inflection points for several vital signs and labs where risk rose substantially. Most notably, patients with median intrapartum systolic blood pressure above 132mmHg had an 11% [interquartile range, 4%] median increase in relative risk for PPH. Conclusions: We developed a novel approach for predicting PPH and identified clinical feature thresholds that can guide intrapartum monitoring for PPH risk. Our results suggest our model is an excellent candidate for prospective evaluation and could ultimately reduce PPH morbidity and mortality through early detection and prevention.
Depressive rumination is correlated with brain responses during self-related processing

Background: Rumination, a tendency to focus on negative self-related thoughts, is a central symptom of depression. Studying the self-related aspect of such symptoms is challenging due to the need to distinguish self effects per se from the emotional content of task stimuli. This study employs an emotionally neutral self-related paradigm to investigate possible altered self processing in depression and its link to rumination. Methods: People with unipolar depression (MDD; n = 25) and controls (n = 25) underwent task-based EEG recording. Late event-related potentials were studied along with low frequency oscillatory power. EEG metrics were compared between groups and correlated with depressive symptoms and reported rumination. Results: The MDD group displayed a difference in late potentials across fronto-central electrodes between self-related and non-self-related conditions. No such difference was seen in controls. The magnitude of this difference was positively related with depressive symptoms and reported rumination. MDD also had elevated theta oscillation power at central electrodes in self-related conditions, which was not seen in controls. Conclusions: Rumination appears linked to altered self-related processing in depression, independently of stimuli-related emotional confounds. This connection between self-related processing and depression may point to self-disorder being a core component of the condition.
Self-employment and Subjective Well-Being

Self-employment contributes to employment growth and innovativeness and many individuals want to become self-employed due to the autonomy and flexibility it brings. Using “subjective well-being” as a broad summary measure that evaluates an individual’s experience of being self-employed, the chapter discusses evidence and explanations why self-employment is positively associated with job satisfaction, even though the self-employed often earn less than their employed peers, work longer hours and experience more stress and higher job demands. Despite being more satisfied with their jobs, the self-employed do not necessarily enjoy higher overall life satisfaction, which is due to heterogeneity of types of self-employment, as well as motivational factors, work characteristics and institutional setups across countries.
Chemistry Acceleration Modeling of Detonation Based on the Dynamical Storage/Deletion Algorithm

A dynamical storage/deletion algorithm with nodal deletion and global deletion modes, originally based on the in situ adaptive tabulation technique, is proposed to accelerate chemistry computations in reactive flows with high Mach number. The algorithm allows for the approximations of the chemical reaction through retrieving nodes stored in a table and deleting nodes during computations. The algorithm is applied to the C3H8/air detonation induced by shock wave focusing. The computational results show the potential advantage of the node removal or table deletion in the simulation of multi-dimensional unsteady detonations. The nodal deletion mode proposed in the present work has a higher speed-up factor of computations than the global deletion mode due to the reservation of nodes, which has a high retrieval frequency in the table. At the specified error tolerance of node approximation, the efficiency of algorithm is dependent on the deletion modes and the table size, without losing the computational accuracy.
A study of water circulation along the Egyptian Mediterranean coast using a three dimensional numerical model

The Egyptian Mediterranean coast lies between longitudes 25° 30' E. and 34° E and extends northward to latitude of 33° N. Its water volume is 224,801.55 km3, and has a surface area of about 154,840 km2. Striking features of this area are the presence of different water masses which converge and mix. The Princeton Ocean Model (POM), which makes use of a curvilinear orthogonal grid and of a sigma‐coordinate system, was used to study the general circulation of the Egyptian Mediterranean waters. The model bathymetry was obtained from the bilinear interpolation of the depth data into the model grid. The model grid contains 35 × 11 points with a resolution ranges from 22 to 27 km. The model has three open boundaries to the west, east and north.