Miracle-dz/UniFAR-FTUs huggingface dataset:
The association of types, intensities and frequencies of physical activity with primary infertility among females in Gaza Strip, Palestine: A case-control study

Introduction Physical activity and energy state balance have fundamentally been related to reproductive system and health. This study explored the relationship between different types, intensities and frequencies of physical activity with primary infertility among women in Gaza Strip, Palestine. Methods A case-control study was conducted in Gaza Strip with the participation of 320 married couples. 160 infertile couples were chosen from five fertility centers registries from 2016 to 2018 and matched residentially with 160 fertile couples. Cases were selected through systematic stratified sampling of five lists categorized according to residency and the determined percentage selected from each list was proportional. Data were collected through a self-administered questionnaire extended by the short form of international physical activity questionnaire and analyzed through SPSS program version 22 by using descriptive analysis, independent T-test, cross-tabulation, and binary logistic regression. Results Low frequency, intensity and duration of physical activity were associated with 3.1 risk of primary infertility (95% CI, 1.60–5.99, P < 0.001). Adjustment for age, marital age, age of menarche, refugee status and monthly income provided 3.2 risk (95% CI, 1.55–6.60, P = 0.002). Women spending more than 300 minutes a day sedentarily were 2.3 times more likely to have fertility problems than physically active females. Measuring energy expenditure in MET-min/w (Metabolic Equivalent) showed vigorous MET-min/w as negatively associated with the infertility status of females (Interquartile range IQR: 480 for cases and 720 for controls, P = 0.010). On the basis of energy expended in kilocalories in relation to weight, results showed the same association (IQR: 564 for case and 864 for controls, P = 0.011). No associations were found between moderate activity levels and primary infertility. Conclusion Low levels of physical activity and sedentary lifestyle endanger the fertility status of females in Gaza Strip. This may offer the need for endorsing and formalizing adequate physical activity education and awareness protocols in the national reproductive health guidelines and empowering environmental capacity building to alter physical activity-related cultural norms.
How Can the Lived Environment Support Healthy Ageing? A Spatial Indicators Framework for the Assessment of Age-Friendly Communities

The Age-Friendly Cities and Communities Guide was released by the World Health Organization over a decade ago with the aim of creating environments that support healthy ageing. The comprehensive framework includes the domains of outdoor spaces and buildings, transportation, housing, social participation, respect and inclusion, civic participation and employment, communication and information, and community and health services. A major critique of the age-friendly community movement has argued for a more clearly defined scope of actions, the need to measure or quantify results and increase the connections to policy and funding levers. This paper provides a quantifiable spatial indicators framework to assess local lived environments according to each Age-Friendly Cities and Communities (AFC) domain. The selection of these AFC spatial indicators can be applied within local neighbourhoods, census tracts, suburbs, municipalities, or cities with minimal resource requirements other than applied spatial analysis, which addresses past critiques of the Age-Friendly Community movement. The framework has great potential for applications within local, national, and international policy and planning contexts in the future.
What is the Nature and Intended Use of Design Methods?

Interest in the codification and application of design methods is rapidly growing as businesses increasingly utilize “design thinking” approaches. However, in this uptake of design methods that encourage designerly action, the ontological status of design methods is often diffuse, with contradictory messages from practitioners and academics about the purpose and desired use of methods within a designer’s process. In this paper, I explore the paradoxical nature of design methods, arguing for a nuanced view that includes the (often) conflicting qualities of prescription and performance. A prescriptive view of methods is drawn from the specification of methods and their “proper” use in the academic literature, while a performative view focuses on in situ use in practice, describing how practitioners use methods to support their everyday work. The ontological characteristics and practical outcomes of each view of design methods are considered, concluding with productive tensions that juxtapose academia and practice.
Phase II Trial of Neoadjuvant Carboplatin and Nab-Paclitaxel in Patients with Triple Negative Breast Cancer.

BACKGROUND In this phase II clinical trial, we evaluated the efficacy of the non-anthracycline combination of carboplatin and nab-paclitaxel in early stage triple negative breast cancer (TNBC). PATIENTS AND METHODS Patients with newly diagnosed stage II-III TNBC (N=69) were treated with neoadjuvant carboplatin (AUC 6) every 28 days x 4 plus nab-paclitaxel (100 mg/m2 ) weekly for 16 weeks. Pathological complete response (pCR) and residual cancer burden (RCB) were analyzed with germline mutation status, tumor infiltrating lymphocytes (TILs), TNBC molecular subtype, and GeparSixto immune signature (GSIS). RESULTS Sixty-seven patients were evaluable for safety and response. Fifty-three (79%) patients experienced grade 3/4 adverse events (AEs), including Grade 3 anemia (43%), neutropenia (39%), leukopenia (15%), thrombocytopenia (12%), fatigue (7%), peripheral neuropathy (7%), neutropenia (16%), and leukopenia (1%). Twenty-four patients (35%) had at least one dose delay and 50 patients (72%) required dose reduction. Sixty-three (94%) patients completed scheduled treatment. The responses were 32/67 (48%) pCR (RCB 0), 10/67 (15%) RCB I, 19/67 (28%) RCB II, 5/67 (7%) RCB III, and 1/67 (2%) progressed and had no surgery. Univariate analysis showed GSIS "immune-hot" and DNA repair defect (DRD) were associated with higher pCR with odds ratio of 4.62 (P=0.005) and 4.76 (P=0.03) respectively, and with RCB 0/I vs. RCB II/III with odds ratio 4.80 (P=0.01). "Immune-hot" GSIS was highly correlated with DRD status (P=0.03), TILs level (P<0.001), and TNBC molecular subtype (P<0.001). After adjusting for age, race, stage, and grade, GSIS remained associated with higher pCR and RCB class 0/I vs. II/III with odds ratio 7.19 (95% CI 2.01-25.68, P=0.002) and 8.95 (95%. CI 2.09-38.23, P=0.003), respectively. CONCLUSIONS The combination of carboplatin and nab-paclitaxel for early stage high risk TNBC showed manageable toxicity and encouraging anti-tumor activity. GSIS "immune-hot" signature is associated with higher pCR rate and RCB class 0/1. This study provides additional rationale for using non-anthracycline platinum-based therapy for future neoadjuvant trials in early stage TNBCs. IMPLICATIONS FOR PRACTICE Platinum is an important neoadjuvant chemotherapy agent for treatment of early stage triple negative breast cancer (TNBC). In this study, carboplatin and nab-paclitaxel were well tolerated and highly effective in TNBC, resulting in pathological complete response of 48%. In univariate and multivariate analyses adjusting for age, race, tumor stage and grade, "immune-hot" GeparSixto Immune Signature (GSIS) and DNA repair defect were associated with higher pCR and residual cancer burden class 0/1. The association of GSIS "immune-hot" signature with higher pCR holds promise for "de-escalating" neoadjuvant chemotherapy for patients with early stage TNBC. Although GSIS is not routinely used in clinic, further development of this immune signature into a clinically applicable assay is indicated.
Accumulation of Phenolic Acids during Storage over Differently Handled Fresh Carrots

Carrots contain a significant content of phenolic compounds, mainly phenolic acids. Technological processing of carrots inflicts wounding stress and induces accumulation of these compounds, especially caffeic acid derivatives, in the periderm tissue. In this study, the effect of minimal processing (polishing, washing, peeling, and grating) on the retention of soluble phenolic acids in carrots was monitored during cold storage. Storage for up to 4 weeks and 24 h was used for whole and grated carrot samples, respectively. Total phenolic acid levels found in differently processed carrots varied greatly at the beginning of the storage period and on dry weight basis they ranged from 228 ± 67.9 mg/kg (grated carrot) to 996 ± 177 mg/kg (machine washed). In each case, processing followed by storage induced phenolic acid accumulation in the carrots. At the end of the experiment (4 weeks at +8 °C), untreated and machine-washed carrots contained ca. 4-fold more phenolic acids than at day 0. Similarly, polished carrots contained 9-fold and peeled carrots 31-fold more phenolic acids than at day 0. The phenolic acid content in grated carrot doubled after 24 h storage at +4 °C. Individual phenolic acids were characterized by high resolution mass spectrometry. MS data strongly suggest the presence of daucic acid conjugates of phenolic acids in carrot. Storage time did not have statistically similar effect on all compounds and generally in a way that dicaffeoyldaucic acid had the highest increase. This research provides important information for primary production, packaging, catering, the fresh-cut industry and consumers regarding the selection of healthier minimally processed carrots.
Conditioning Machine Learning Models to Adjust Lowbush Blueberry Crop Management to the Local Agroecosystem

Agroecosystem conditions limit the productivity of lowbush blueberry. Our objectives were to investigate the effects on berry yield of agroecosystem and crop management variables, then to develop a recommendation system to adjust nutrient and soil management of lowbush blueberry to given local meteorological conditions. We collected 1504 observations from N-P-K fertilizer trials conducted in Quebec, Canada. The data set, that comprised soil, tissue, and meteorological data, was processed by Bayesian mixed models, machine learning, compositional data analysis, and Markov chains. Our investigative statistical models showed that meteorological indices had the greatest impact on yield. High mean temperature at flower bud opening and after fruit maturation, and total precipitation at flowering stage showed positive effects. Low mean temperature and low total precipitation before bud opening, at flowering, and by fruit maturity, as well as number of freezing days (<−5 °C) before flower bud opening, showed negative effects. Soil and tissue tests, and N-P-K fertilization showed smaller effects. Gaussian processes predicted yields from historical weather data, soil test, fertilizer dosage, and tissue test with a root-mean-square-error of 1447 kg ha−1. An in-house Markov chain algorithm optimized yields modelled by Gaussian processes from tissue test, soil test, and fertilizer dosage as conditioned to specified historical meteorological features, potentially increasing yield by a median factor of 1.5. Machine learning, compositional data analysis, and Markov chains allowed customizing nutrient management of lowbush blueberry at local scale.
Portal dosimetry scripting application programming interface (PDSAPI) for Winston‐Lutz test employing ceramic balls

Abstract Purpose Stereotactic radiosurgery (SRS) and stereotactic body radiation therapy (SBRT) treatments require a high degree of accuracy. Mechanical, imaging, and radiation isocenter coincidence is especially important. As a common method, the Winston‐Lutz (WL) test plays an important role. However, weekly or daily WL test can be very time consuming. We developed novel methods using Portal Dosimetry Scripting Application Programming Interface (PDSAPI) to facilitate the test as well as documentation. Methods Winston‐Lutz PDSAPI was developed and tested on our routine weekly WL imaging. The results were compared against two commercially available software RIT (Radiological Imaging Technology, Colorado Springs, CO) and DoseLab (Varian Medical Systems, Inc. Palo Alto, CA). Two manual methods that served as ground truth were used to verify PDSAPI results. Twenty WL test image data sets (10 fields per tests, and 200 images in total) were analyzed by these five methods in this report. Results More than 99.5% of WL PDSAPI 1D shifts agreed with each of four other methods within ±0.33 mm, which is roughly the pixel width of a‐Si 1200 portal imager when source to imager distance (SID) is at 100 cm. 1D shifts agreement for ±0.22 mm and 0.11 mm were 96% and 63%, respectively. Same trend was observed for 2D displacement. Conclusions Winston‐Lutz PDSAPI delivers similar accuracy as two commercial applications for WL test. This new application can save time spent transferring data and has the potential to implement daily WL test with reasonable test time. It also provides the data storage capability, and enables easy access to imaging and shift data.
Phthalates and Bisphenol A: Presence in Blood Serum and Follicular Fluid of Italian Women Undergoing Assisted Reproduction Techniques

Background: folliculogenesis is a strictly regulated process that may be affected by endocrine disrupting chemicals (EDCs) through sometimes not so clear molecular mechanisms. Methods: we conducted a multicentric observational study involving six fertility centers across Italy, prospectively recruiting 122 women attending a fertility treatment. Recruited women had age ≤42 years, and normal ovarian reserve. Blood and follicular fluid samples were taken for EDCs measurement using liquid chromatography tandem mass spectrometry and each woman completed an epidemiological questionnaire. Results: The main EDCs found were monobutyl phthalate (MBP) (median blood: 8.96 ng/mL, follicular fluid 6.43 ng/mL), monoethylhexyl phthalate (MEHP) (median blood: 9.16 ng/mL, follicular fluid 7.68 ng/mL) and bisphenol A (BPA) (median blood: 1.89 ng/mL, follicular fluid 1.86 ng/mL). We found that serum MBP concentration was significantly associated with the considered area (p < 0.001, adj. mean: 7.61 ng/mL, 14.40 ng/mL, 13.56 ng/mL; Area 1: Milan–Turin, Area 2: Rome–Naples; Area 3: Catania–Bari, respectively) but negatively with home plastic food packaging (p = 0.004). Follicular MBP was associated with irregular cycles (p = 0.019). No association was detected between EDCs and eating habits and other clinical and epidemiological features. Conclusions: This study represents the first Italian biomonitoring of plastic EDCs in follicular fluid, laying the basis for future prospective evaluation on oocyte quality before assisted reproduction techniques (ART).
Structural Basis for Misfolding at Disease Phenotypic Positions in CFTR

Misfolding of membrane proteins as a result of mutations that disrupt their functions in substrate transport across the membrane or signal transduction is the cause of many significant human diseases. Yet, we still have a limited understanding of the direct consequences of these mutations on folding and function a necessary step toward the rational design of corrective therapeutics. This thesis addresses the gap in understanding the residue-specific implications for folding through a series of experiments that utilize the cystic fibrosis transmembrane conductance regulator (CFTR) as a model in various contexts. We first examined the thermodynamic implications of mutations in the soluble nucleotide binding domain 1 (NBD1) of CFTR. We found that mutations can have a significant effect on thermodynamic stability that is masked in non-physiological conditions. Our studies were then focussed on a membraneembedded hairpin CFTR fragment comprised of transmembrane segments 3 (TM3) and 4 (TM4) to evaluate the direct effects of mutations on folding in a systematic manner. It was found that the translocon-mediated membrane insertion of helices closely parallels a basic hydrophobicaqueous partitioning event. This study was then extended to determine residue-specific effects on helix-helix association. We found that this process is not solely dependent on hydropathy, but there is a context dependence of these results with regard to residue position within the helix. iii Overall, these findings constitute a key step in relating mutation-derived effects on membrane protein folding to the underlying basis of human disease such as cystic fibrosis.
Model reduction using the AISIAD algorithm

Many powerful linear systems and control theory tools have been out of the reach of the fluids community due to the complexity of the Navier-Stokes equations. Flow control based on systematic methods adopted from control theory is becoming a fairly mature field, with both computational and experimental advances. In this sense, model reduction plays an important role in developing effective control strategies for practical applications, since the dynamical systems which describe most flows are discretized partial differential equations with many degrees of freedom. Currently, balanced truncation represents the standard method of model reduction in systems and control theory which preserves the main input-output characteristics of the system. In this article we investigate an approximate balanced truncation by applying a modified version of the AISIAD algorithm [4]. The method is demonstrated on the Ginzburg-Landau equation and the linearized flow in a plane channel.
Safety and Efficacy With Augmented Second-Generation Perforated Pedicle Screws in Treating Degenerative Spine Disease in Elderly Population

ABSTRACT Background: Degenerative spine disease is a common cause of low back pain in people age 65 years or older. Nonsurgical treatment is tried first, but if it is unsuccessful, surgery is advocated. This has special connotations for both underlying disease and the biomechanical characteristics of osteoporotic bone. We conducted an observational study to investigate the clinical and radiological outcome in patients in this age group with poor bone quality and degenerative lumbar instability treated with fusion using perforated pedicle screws augmented with polymethylmethacrylate (PMMA). Methods: We collected prospective data on treatment, outcome, and patient characteristics from our institution's database. The primary outcome was a change in pain and physical function measured by the visual analog scale, the Core Outcome Measures Index, and the Oswestry Disability Index. Control participants were also analyzed for secondary complications such as hardware mobilization, fusion (as apparent on radiographs), and adjacent fractures or adjacent degenerative disc disease. Results: We included 89 patients who underwent surgery between October 2015 and February 2018 at a mean age of 78 years (range, 67–88 years) and were then monitored for at least 12 months (range, 12–40 months). Findings on pain and function questionnaires showed improvement at 6 months after surgery, maintained at the final evaluation; 90% of patients had final score increases of ≥15 points. No patient developed clinical complications secondary to PMMA leakages. One patient had nonunion and screw breakage. No other patient had clinical or radiological nonunion. Of the control participants, 6 had adjacent disc disease, with 2 of them requiring instrumentation extension. Six deep infections required surgical revision without removal of material. Conclusion: PMMA-augmented cannulated pedicle screw instrumentation in spine fusion effectively and safely treats degenerative lumbar disease in patients who are age 65 years or older with poor bone quality.
Neuromodulatory Control and Language Recovery in Bilingual Aphasia: An Active Inference Approach

Understanding the aetiology of the diverse recovery patterns in bilingual aphasia is a theoretical challenge with implications for treatment. Loss of control over intact language networks provides a parsimonious starting point that can be tested using in-silico lesions. We simulated a complex recovery pattern (alternate antagonism and paradoxical translation) to test the hypothesis—from an established hierarchical control model—that loss of control was mediated by constraints on neuromodulatory resources. We used active (Bayesian) inference to simulate a selective loss of sensory precision; i.e., confidence in the causes of sensations. This in-silico lesion altered the precision of beliefs about task relevant states, including appropriate actions, and reproduced exactly the recovery pattern of interest. As sensory precision has been linked to acetylcholine release, these simulations endorse the conjecture that loss of neuromodulatory control can explain this atypical recovery pattern. We discuss the relevance of this finding for other recovery patterns.
University Student Perspectives of Entomophagy: Positive Attitudes Lead to Observability and Education Opportunities

Abstract Positive experiences with insect food items that highlight the benefits of insect production and reduce the novelty of entomophagy are needed. Toward this goal, we developed an experiential learning lesson plan that would provide a positive experience with entomophagy and associate key educational content related to insect food items. First, two cricket powder brownie taste-test surveys were conducted with groups of university students to evaluate attitudes relating to insects as food, sustainability of insect production, and nutritional content. Students displayed a taste preference for cricket flour brownies but could not consistently differentiate between brownie types, ranked environmental and nutritional benefits associated with insect food products over taste factors alone, and indicated a positive attitude toward purchasing insect products in the future. Willingness to try other insect products in the future was significantly greater for students with increased experience with consuming insect products. These results were then used to create an university lesson plan that will allows for future evaluation of student attitudes while increasing exposure to entomophagy and providing education on the positive aspects of insects as food production. Our work highlights the favorable attitude toward insect food products shown by university students and how positive perception of entomophagy increases with continued exposure to the practice.