Miracle-dz/UniFAR-FTUs huggingface dataset:
A software framework for control and automation of precisely timed experiments

Advanced physics experiments require computer control systems to coordinate the apparatus on time scales from hours to nanoseconds. In this thesis I present a new software system, the labscript suite, for controlling modern ultracold atom experiments. Labscript prepares experiments from Python code and a list of parameters, generating instructions for heterogeneous hardware: pulse sequencers, analog input/output, and radio-frequency synthesis devices, which in turn execute the experiment in strict real time. Other software components automate scheduling of long-running experimental sequences, and the analysis of results. The labscript suite rapidly creates sophisticated experiments, flexibly analyses results, and archives the data.
Small, Smaller, Smallest: Minimal Structural Requirements for a Fully Functional Box C/D Modification Guide RNA

Site-specific 2’-O-ribose methylation is an abundant post-transcriptional modification mediated by small non-coding nuclear RNAs known as box C/D modification guide RNAs. The minimal structural requirements for these guide RNAs to function in higher eukaryotes are still unclear. To address this question, we generated a series of mutant variants of Drosophila box C/D scaRNA:MeU2-C28 and tested their modification guide activities in the Xenopus oocyte system. Our data suggest that box C/D guide RNA function requires either a terminal or an internal consensus kink-turn structure. We identified the minimal functional box C/D guide RNA. It consists of a single-domain molecule with (i) a terminal stem with a consensus kink-turn domain, (ii) one box C and box D connected by a 14-nucleotide antisense element and (iii) a one-nucleotide spacer between the box C and the antisense element. In this single domain RNA, the sequence of the spacer is more important than its length. We suggest that the secondary structure of box C/D RNAs, essential for guide RNA function, is more complex than generally supposed. At the same time, the expression of functional extremely short single-domain box C/D RNAs is possible in higher eukaryotes.
A single-centre investigator-blinded randomised parallel group clinical trial to investigate the effect of probiotic strains Streptococcus salivarius M18 and Lactobacillus acidophilus on gingival health of paediatric patients undergoing treatment with fixed orthodontic appliances: study protocol

Background There is limited data on the beneficial effects of probiotics on the gingival health of patients undergoing treatment with fixed orthodontic appliances. This study aims to compare the effect of probiotic tablets combined with regular oral hygiene versus regular oral hygiene alone on gingival status in these patients. The effect of probiotic intake on plaque formation and salivary microbiome composition will be also assessed. Methods and analysis This is a 3 month single-centre, single blind (clinical and laboratory examiners), parallel group randomised controlled two arm superiority trial. Fifty paediatric patients attending the Postgraduate Orthodontic Clinic at the Hamdan Bin Mohammed College of Dental Medicine (HBMCDM), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Dubai, United Arab Emirates, who meet the eligibility criteria will be recruited. Block randomisation with 1:1 allocation and concealment of allocation will be carried out. The treatment group will receive probiotic tablets containing Streptococcus salivarius M18 and Lactobacillus acidophilus together with regular oral hygiene versus the control group on regular oral hygiene alone. Clinical examination and collection of saliva for microbiome assay will be carried out at baseline and end of study. Self-reporting by patients will be used to document acceptability and adverse effects. Statistically significant decrease in gingival bleeding on probing in the treatment group will be classified as primary outcome of treatment success. Statistically significant reduction in Plaque Index, Gingival Index and shift in the composition of the oral microbiome in favour of beneficial bacteria are secondary outcomes indicative of efficacy of probiotic intake. Ethics and dissemination Ethical approval for the study has been granted by the HBMCDM, MBRU, Institutional Review Board (Reference #: MBRU-IRB-2018–015). Study findings will be disseminated via publication in peer-reviewed journal. Trial registration number ISRCTN95085398
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Usability evaluation methods (UEMs) are widely recognised as an essential part of systems development. Assessments of the performance of UEMs, however, have been criticised for low validity and limited reliability. The present study extends this critique by describing seven dogmas in recent work on UEMs. The dogmas include using inadequate procedures and measures for assessment, focusing on win–lose outcomes, holding simplistic models of how usability evaluators work, concentrating on evaluation rather than on design and working from the assumption that usability problems are real. We discuss research approaches that may help move beyond the dogmas. In particular, we emphasise detailed studies of evaluation processes, assessments of the impact of UEMs on design carried out in real-world systems development and analyses of how UEMs may be combined.
Use of Unmanned Aerial Vehicle Imagery and Deep Learning UNet to Extract Rice Lodging

Rice lodging severely affects harvest yield. Traditional evaluation methods and manual on-site measurement are found to be time-consuming, labor-intensive, and cost-intensive. In this study, a new method for rice lodging assessment based on a deep learning UNet (U-shaped Network) architecture was proposed. The UAV (unmanned aerial vehicle) equipped with a high-resolution digital camera and a three-band multispectral camera synchronously was used to collect lodged and non-lodged rice images at an altitude of 100 m. After splicing and cropping the original images, the datasets with the lodged and non-lodged rice image samples were established by augmenting for building a UNet model. The research results showed that the dice coefficients in RGB (Red, Green and Blue) image and multispectral image test set were 0.9442 and 0.9284, respectively. The rice lodging recognition effect using the RGB images without feature extraction is better than that of multispectral images. The findings of this study are useful for rice lodging investigations by different optical sensors, which can provide an important method for large-area, high-efficiency, and low-cost rice lodging monitoring research.
Submental Island Flap versus Free Flap Reconstruction for Complex Head and Neck Defects

Objective Complex soft tissue reconstruction of the head and neck requires a viable, versatile, and dependable flap. Free flaps, such as the radial forearm and anterolateral thigh flap, have been the mainstay of complex head and neck reconstruction. However, a local pedicled flap, such as the submental island flap (SIF), could be a more effective and less demanding alternative. This systematic review and meta-analysis aim to compare free tissue transfer (FTT) with the SIF for head and neck reconstruction. Data Sources We performed a systematic search in PubMed and EMBASE databases. Meta-analysis was performed on outcomes reported in ≥3 studies. Review Methods Candidate articles were assessed for eligibility by 2 authors. Three authors performed data extraction and methodological quality of the included studies using the Newcastle-Ottawa Quality Assessment Form for Cohort Studies. Results The search strategy resulted in 450 studies, of which 7 were included in the analysis, yielding 155 SIF and 198 FTT cases. Operating time and length of stay were significantly lower for the SIF than for FTT (P = .05 and P = .0008). There was no significant difference between the groups for complete flap loss, debulking revisions, and oncologic recurrence. Conclusion These results suggest that the SIF reduces length of stay and operating time as compared with FTT in head and neck reconstruction. These findings suggest that the SIF can be considered an alternative reconstructive option to FTT when evaluating intraoral, lateral facial, skull base, and parotidectomy defects, given comparable defect size and tumor biology.
Vitamin D Modulates the Response of Bronchial Epithelial Cells Exposed to Cigarette Smoke Extract

In chronic obstructive pulmonary disease (COPD), the bronchial epithelium is the first immune barrier that is triggered by cigarette smoke. Although vitamin D (vitD) has proven anti-inflammatory and antimicrobial effects in alveolar macrophages, little is known about the direct role of vitD on cigarette smoke-exposed bronchial epithelial cells. We examined the effects of vitD on a human bronchial epithelial cell line (16HBE) and on air–liquid culture of primary bronchial epithelial cells (PBEC) of COPD patients and controls exposed for 24 h to cigarette smoke extract (CSE). VitD decreased CSE-induced IL-8 secretion by 16HBE cells, but not by PBEC. VitD significantly increased the expression of the antimicrobial peptide cathelicidin in 16HBE and PBEC of both COPD subjects and controls. VitD did not affect epithelial to mesenchymal transition or epithelial MMP-9 expression and was not able to restore impaired wound healing by CSE in 16HBE cells. VitD increased the expression of its own catabolic enzyme CYP24A1 thereby maintaining its negative feedback. In conclusion, vitD supplementation may potentially reduce infectious exacerbations in COPD by the upregulation of cathelicidin in the bronchial epithelium.
Epidemiología de la enfermedad glomerular en adultos. Revisión de una base de datos

La enfermedad glomerular esta dentro de las primeras 10 causas de muerte en Mexico. Objetivo: Determinar la frecuencia de glomerulopatias en el occidente de Mexico, en un hospital de segundo nivel del IMSS. Material y metodos: Analisis retrospectivo de un centro hospitalario. Se revisaron todas las biopsias de rinon nativo de enero de 2003 a diciembre de 2011, de pacientes mayores de 16 anos, estableciendo las caracteristicas clinicas, la forma de presentacion y el reporte histopatologico. Resultados: Se analizaron 163 reportes de biopsias; el promedio de edad de los pacientes fue de 32.6 ± 13.3 anos; hubo un 55% de mujeres. El 24% presentaron hipertension arterial sistemica (HAS) y el 10%, antecedentes familiares de insuficiencia renal cronica. Las glomerulonefritis (GMN) primarias mas frecuentes fueron la glomeruloesclerosis focal y segmentaria (GEFyS) (47%) y la GMN membranosa (15%). Las GMN secundarias mas frecuentes fueron la nefropatia lupica (NL) (14%), la amiloidosis (1.2%) y la nefropatia diabetica (ND) (4%). Conclusion: La GEFyS es la glomerulopatia mas frecuente; se observa menor porcentaje de nefropatia por deposito de inmunoglobulina A (NIgA) que lo reportado a nivel mundial. La informacion presentada aqui es una contribucion al entendimiento de la prevalencia de glomerulopatia en el occidente de Mexico
Real-Time Pricing for Smart Grid with Multiple Companies and Multiple Users Using Two-Stage Optimization

Abstract In this paper, we focus on the real-time interactions among multiple utility companies and multiple users and formulate real-time pricing (RTP) as a two-stage optimization problem. At the first stage, based on cost function, we propose a continuous supply function bidding mechanism to model the utility companies’ profit maximization problem, by which the analytic expression of electricity price is further derived. At the second stage, considering that individually optimal solution may not be socially optimal, we employ convex optimization with linear constraints to model the price anticipating users’ daily payoff maximum. Substitute the analytic expression of electricity price obtained at the first stage into the optimization problem at the second stage. Using customized proximal point algorithm (C-PPA), the optimization problem at the second stage is solved and electricity price is obtained accordingly. We also prove the existence and uniqueness of the Nash equilibrium in the mentioned two-stage optimization and the convergence of C-PPA. In addition, in order to make the algorithm more practical, a statistical approach is used to obtain the function of price only through online information exchange, instead of solving it directly. The proposed approach offers RTP, power production and load scheduling for multiple utility companies and multiple users in smart grid. Statistical approach helps to protect the company’s privacy and avoid the interference of random factors, and C-PPA has an advantage over Lagrangian algorithm because the former need not obtain the objection function of the dual optimization problem by solving an optimization problem with parameters. Simulation results show that the proposed framework can significantly reduce peak time loading and efficiently balance system energy distribution.
The Phosphatase SHP-2 Activates HIF-1α in Wounds In Vivo by Inhibition of 26S Proteasome Activity

Vascular remodeling and angiogenesis are required to improve the perfusion of ischemic tissues. The hypoxic environment, induced by ischemia, is a potent stimulus for hypoxia inducible factor 1α (HIF-1α) upregulation and activation, which induce pro-angiogenic gene expression. We previously showed that the tyrosine phosphatase SHP-2 drives hypoxia mediated HIF-1α upregulation via inhibition of the proteasomal pathway, resulting in revascularization of wounds in vivo. However, it is still unknown if SHP-2 mediates HIF-1α upregulation by affecting 26S proteasome activity and how the proteasome is regulated upon hypoxia. Using a reporter construct containing the oxygen-dependent degradation (ODD) domain of HIF-1α and a fluorogenic proteasome substrate in combination with SHP-2 mutant constructs, we show that SHP-2 inhibits the 26S proteasome activity in endothelial cells under hypoxic conditions in vitro via Src kinase/p38 mitogen-activated protein kinase (MAPK) signalling. Moreover, the simultaneous expression of constitutively active SHP-2 (E76A) and inactive SHP-2 (CS) in separate hypoxic wounds in the mice dorsal skin fold chamber by localized magnetic nanoparticle-assisted lentiviral transduction showed specific regulation of proteasome activity in vivo. Thus, we identified a new additional mechanism of SHP-2 mediated HIF-1α upregulation and proteasome activity, being functionally important for revascularization of wounds in vivo. SHP-2 may therefore constitute a potential novel therapeutic target for the induction of angiogenesis in ischemic vascular disease.
The association between 24-h blood pressure patterns and left ventricular mechanics.

OBJECTIVE We sought to investigate left ventricular (LV) mechanics in the recently diagnosed hypertensive patients with different 24-h blood pressure (BP) patterns (dipping, nondipping, extreme dipping and reverse dipping). METHODS The current cross-sectional study included 209 hypertensive patients who underwent 24-h ambulatory BP monitoring and comprehensive two-dimensional echocardiographic examination including multilayer strain analysis. RESULTS There was no difference in 24-h and daytime BP values between four groups. Night-time BP significantly and gradually increased from extreme dippers, across dippers and nondippers, to reverse dippers. LV global longitudinal and circumferential strains were greater in dippers and extreme dippers than in nondippers and reverse dippers. This was also found for endocardial and epicardial LV longitudinal and circumferential strains. Multivariate logistic regression analysis demonstrated that nondipping and reverse dipping patterns were associated with reduced LV longitudinal strain [odds ratio (OR) 1.71 (95% confidence interval (CI): 1.10-5.61) and OR 2.50 (95% CI: 1.31-6.82), respectively] independently of age, sex, 24-h SBP, LV mass index and E/è. Only the reverse dipping BP pattern was independently of clinical and echocardiographic parameters related with reduced LV circumferential strain [OR 1.90 (95% CI: 1.10-4.80)]. CONCLUSION Nondipping and reverse dipping BP patterns had stronger impact on LV mechanics compared with patients with dipping and extreme dipping BP patterns in hypertensive population. LV functional and mechanical remodeling deteriorated from extreme dippers and dippers, to nondippers and reverse dippers.
Cellphone-Based Automated Fugl-Meyer Assessment to Evaluate Upper Extremity Motor Function After Stroke

The Fugl-Meyer Assessment (FMA) is a widely used evaluation tool for assessing upper extremity motor function during stroke rehabilitation. However, the FMA is a repetitive, time-consuming task that currently must be performed by therapists in a hospital or clinic. We thus propose an alternative automated approach in which patients perform FMA movements while holding a cellphone at the hand and receive automated FMA scores. In the proposed system, features are extracted from cellphone movement data and decision trees are used to automatically score FMA test items. Ten stroke patients with upper extremity dysfunction participated in a validation experiment to compare automated FMA scores with traditional FMA scores from a trained therapist. Results showed that FMA scores from the cellphone-based automated system were highly correlated with FMA scores from the trained therapist (r2 = 0.97), and that the average accuracy for individual FMA test items was 85%. These results demonstrate that such a portable, automated FMA system could potentially be used to assess upper extremity function during stroke rehabilitation to remove the repetitive, time-consuming burden from therapists and could potentially be performed in clinic or home-based settings.
Inhaled Kathon may induce eosinophilia‐mediated disease in the lung

In 2011, a link between humidifier disinfectants and patients with idiopathic pulmonary fibrosis was identified in Korea, and Kathon was suggested as one of the causative agents. In this study, Kathon induced apoptotic cell death along with membrane damage at 24 h post‐exposure. Additionally, on day 14 after a single instillation with Kathon, the total number of pulmonary cells and the levels of TNF‐α, IL‐5, IL‐13, MIP‐1α, and MCP‐1α clearly increased in the lung of mice. The proportion of natural killer cells and eosinophils were significantly elevated in the spleen and the bloodstream, respectively, and the level of immunoglobulin (Ig) A, but not IgG, IgM, and IgE, dose‐dependently increased. Therefore, we suggest that inhaled Kathon may induce eosinophilia‐mediated disease in the lung by disrupting homeostasis of pulmonary surfactants. Considering that eosinophilia is closely related to cancer and fibrosis, further studies are needed to understand the relationship between them.
After the Burden is Lifted: Caregivers' Recovery of Life Satisfaction after The Death or Recovery of a Spouse.

OBJECTIVE How do caregivers' life satisfaction shift upon the recovery of an ill spouse? Paradoxically, there is a greater increase in life satisfaction upon death than recovery of a spouse. Our analysis explores this paradox. METHOD We follow the two groups of exiting caregivers longitudinally for four years from when the partner is still in need of care until the death (N= 152) or recovery (N= 112) of a previously ill partner, comparing their trajectory of life satisfaction. We use the years 2001-2016 of the German-Socio-Economic Panel Study and a growth-curve analysis. RESULTS Contrary to our expectations, bereaved caregivers experience a significantly stronger increase in life satisfaction than spouses whose partners recover from a serious illness, even when we stratify by age, gender and initial life satisfaction to account for significantly different subsample composition. Surprisingly, life satisfaction remains unchanged when the partner recovers. Only if a heavy burden in terms of unpaid care and housework hours or prior care need is lifted, do we observe an increase in life satisfaction among spouses with recovering partners, which is like the one experienced by bereaved caregivers.
Comparison of Dry Versus Wet Milling to Improve Bioethanol or Methane Recovery from Solid Anaerobic Digestate

Biogas plants for waste treatment valorization are presently experiencing rapid development, especially in the agricultural sector, where large amounts of digestate are being generated. In this study, we investigated the effect of vibro-ball milling (VBM) for 5 and 30 min at a frequency of 20 s−1 on the physicochemical composition and enzymatic hydrolysis (30 U g−1 total solids (TS) of cellulase and endo-1,4-xylanase from Trichoderma longibrachiatum) of dry and wet solid separated digestates from an agricultural biogas plant. We found that VBM of dry solid digestate improved the physical parameters as both the particle size and the crystallinity index (from 27% to 75%) were reduced. By contrast, VBM of wet solid digestate had a minimal effect on the physicochemical parameters. The best results in terms of cellulose and hemicelluloses hydrolysis were noted for 30 min of VBM of dry solid digestate, with hydrolysis yields of 64% and 85% for hemicelluloses and cellulose, respectively. At the condition of 30 min of VBM, bioethanol and methane production on the dry solid separated digestate was investigated. Bioethanol fermentation by simultaneous saccharification and fermentation resulted in an ethanol yield of 98 geth kg−1 TS (corresponding to 90% of the theoretical value) versus 19 geth kg−1 TS for raw solid digestate. Finally, in terms of methane potential, VBM for 30 min lead to an increase of the methane potential of 31% compared to untreated solid digestate.
Successful anti‐CD19 CAR T‐cell therapy in HIV‐infected patients with refractory high‐grade B‐cell lymphoma

Cancer November 1, 2019 Herein, we have reported on 2 patients with AIDS-associated, high-grade, B-cell lymphoma who were treated with commercially available anti-CD19 chimeric antigen receptor (CAR) T cells for chemotherapy-refractory disease. CAR T cells are autologous T cells that are apheresed from a patient and then transfected to express a CAR. The CAR includes an extracellular antigen recognition domain derived from an antibody, a transmembrane domain or hinge, and intracellular costimulation and signaling domains that activate the T cell. These genetically modified T cells then are expanded in the laboratory and reinfused into the patient, in whom they can now specifically recognize and destroy tumor cells bearing the target antigen. Two CAR T cells, both of which target the B-cell antigen CD19, currently are approved by the US Food and Drug Administration for the treatment of patients with refractory, aggressive B-cell lymphomas. The first patient initially presented at age 47 years with dysphagia and was found to have a large tonsillar mass. Computed tomography (CT) scans confirmed a large right tonsillar mass and multiple enlarged lymph nodes bilaterally. A biopsy of the tonsillar mass demonstrated diffuse large B-cell lymphoma (DLBCL) of germinal center B-cell subtype. In situ hybridization demonstrated no staining for Epstein-Barr virus (EBV)–encoded RNA. The karyotype was hyperdiploid and contained clonal aberrations including trisomies 2, 7, and 21, as well as 12p deletion, 9q deletion, and 14q deletion, none of which to our knowledge are diagnostically specific for a subtype of lymphoma. A staging positron emission tomography (PET)–CT scan demonstrated multifocal intense uptake in bilateral parotid glands and tonsils, extensive adenopathy above and below the diaphragm, and the involvement of the spleen and bone marrow. Bone marrow biopsy confirmed involvement by large B-cell lymphoma. The disease was classified as Ann Arbor stage IV and the patient’s International Prognostic Index score was 3.