bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation and optimization of functional and antinutritional properties of aquafaba
Authors: Alsalman Fatemah B. , Tulbek Mehmet , Nickerson Michael , Ramaswamy Hosahalli S. 
Published: January 2020

AbstractEgg protein is responsible for the second most serious of all food allergens, which affects predominantly the children. Therefore, a new type of vegan ingredient called “aquafaba,” is getting recognized as a plant‐based emulsifier in many bakery product preparations instead of the conventionally used egg white and is emerging in the consumer market. It is the residue water from cooked chickpeas. In this study, an I‐optimal mixture experimental design is combined with a response surface methodology to evaluate the chickpeas cooking process for obtaining aquafaba. The following variables were used: chickpea to cooking water ratio (CPCWR; 1:2, 1:4, and 2:3) and cook time (15, 30, 45, and 60 min). The principal goal was to maximize the functional properties and protein content, while minimizing tannin and phytate contents of aquafaba. The results showed that both CPCWR and cooking time had significant effect on the responses. Emulsion properties were the maximum at 2:3 CPCWR and cooking time of 60 min. Foaming capacity was highest (120%) at 2:3 CPCWR cooked for 30 min, whereas the foam was most stable (57 min) at 1:2 CPCWR with 45 min cooking. Water holding capacity reached the maximum level when cooked for 15 min, and oil holding capacity maximum was obtained after 60 min cooking. Polynomial models were developed for all 11 responses. Optimal results were achieved under the following conditions: 1.5:3.5 CPCWR and 60 min cook time, and the overall desirability fraction was 0.81. Validation tests confirmed these results.
Spatial and temporal dynamics of pCO2 and CO2 flux in tropical Lake Malawi
Authors: Ngochera Maxon J. , Bootsma Harvey A. 
Published: January 2020

AbstractNumerous studies have documented CO2 dynamics in temperate lakes, but few such studies have been conducted on tropical lakes. Spatial and seasonal variation of air and water pCO2, along with supporting limnological and meteorological variables, were measured aboard a vessel of opportunity along the north–south axis of Lake Malawi. These measurements were used to estimate annual net lake‐atmosphere CO2 flux and infer mechanisms regulating it. Surface pCO2 and CO2 flux varied significantly with season and location. Temporally, the lake was CO2‐undersaturated during the rainy season and the mixing season, and supersaturated at the onset of the mixing season and during the hot, stratified season. Concurrent measurements of lake temperature, weather conditions, phytoplankton biomass, and seston δ13C suggest that periods of net CO2 flux into the lake correspond with higher phytoplankton growth rates resulting from internal nutrient loading in the mixing season and allochthonous nutrient inputs in the rainy season. Unlike the rest of the lake, the southernmost region of the lake was usually CO2 supersaturated even though phytoplankton productivity is highest in this region. While the upwelling of hypolimnetic water at the southern end of the lake is a major source of nutrients that drive phytoplankton photosynthesis and CO2 uptake, the CO2 introduced in upwelled water appears to overwhelm photosynthetic capacity locally, especially at the onset of the mixing season. Lake Malawi appears to be a net CO2 sink with an annual whole‐lake CO2 flux of −2.17 ± 0.25 × 1010 mol C yr−1 and a mean daily CO2 flux of −2.05 ± 0.27 mmol C m−2 d−1. A comparison of deep‐water C : P ratios with epilimnetic seston C : P ratios suggests that P is recycled more efficiently than C in the lake's anoxic hypolimnion, and so P vertical mixing creates a carbon deficit that is met by flux from the atmosphere into the lake.
Biosynthesis and characterization of a recombinant eukaryotic allophycocyanin using prokaryotic accessory enzymes
Authors: Dagnino‐Leone Jorge , Figueroa Maximiliano , Uribe Elena , Hinrichs María Victoria , Ortiz‐López Diego , Martínez‐Oyanedel José , Bunster Marta 
Published: January 2020

AbstractPhycobiliproteins (PBPs) are colored fluorescent proteins present in cyanobacteria, red alga, and cryptophyta. These proteins have many potential uses in biotechnology going from food colorants to medical applications. Allophycocyanin, the simplest PBP, is a heterodimer of αβ subunits that oligomerizes as a trimer (αβ)3. Each subunit contains a phycocyanobilin, bound to a cysteine residue, which is responsible for its spectroscopic properties. In this article, we are reporting the expression of recombinant allophycocyanin (rAPC) from the eukaryotic red algae Agarophyton chilensis in Escherichia coli, using prokaryotic accessory enzymes to obtain a fully functional rAPC. Three duet vectors were used to include coding sequences of α and β subunits from A. chilensis and accessorial enzymes (heterodimeric lyase cpc S/U, heme oxygenase 1, phycocyanobilin oxidoreductase) from cyanobacteria Arthrospira maxima. rAPC was purified using several chromatographic steps. The characterization of the pure rAPC indicates very similar spectroscopic properties, λmaxAbs, λmaxEm, fluorescence lifetime, and chromophorylation degree, with native allophycocyanin (nAPC) from A. chilensis. This method, to produce high‐quality recombinant allophycocyanin, can be used to express and characterize other macroalga phycobiliproteins, to be used for biotechnological or biomedical purposes.
Clinical and Cerebral Metabolic Changes in Parkinson's Disease With Basal Forebrain Atrophy
Authors: Gang Miyeong , Baba Toru , Hosokai Yoshiyuki , Nishio Yoshiyuki , Kikuchi Akio , Hirayama Kazumi , Hasegawa Takafumi , Aoki Masashi , Takeda Atsushi , Mori Etsuro , Suzuki Kyoko 
Published: January 2020

AbstractBackgroundCholinergic dysfunction plays a key role in cognitive dysfunction in Parkinson's disease (PD). Recent studies revealed that atrophy in the nucleus basalis of Meynert (NBM), the largest cholinergic nucleus in the basal forebrain, heralds cognitive decline in PD. Despite clinical importance of NBM atrophy in PD, clinical and radiological correlates of NBM atrophy remains to be elucidated.ObjectiveWe investigated the longitudinal changes in clinical and cerebral glucose metabolic characteristics in PD with atrophy in the NBM.MethodsWe analyzed the 3‐year longitudinal data of 56 PD patients who underwent motor, nonmotor, and imaging evaluations at baseline. The patients were classified into PD with and without NBM atrophy based on the results of magnetic resonance imaging volumetry. We compared clinical characteristics and cerebral glucose metabolic changes between PD with and without NBM atrophy.ResultsAt baseline, 20 patients and 36 patients were classified into PD with and without NBM atrophy groups, respectively. At follow‐up, the data of the 14 PD patients in the NBM atrophy group and the 18 patients in the group without NBM atrophy completed full assessments and were available for the analysis. The PD with NBM atrophy group showed severe cognitive dysfunction and psychiatric symptoms both at baseline and follow‐up. The NBM volume significantly correlated with motor and nonmotor functions. The PD with NBM atrophy showed significantly reduced metabolism in the parietal and occipital cortices both at baseline and follow‐up.ConclusionsBasal forebrain atrophy is a simple and sensible marker of faster disease progression and cortical hypometabolism in PD. © 2020 International Parkinson and Movement Disorder Society
Genome sequencing analysis of a family with a child displaying severe abdominal distention and recurrent hypoglycemia
Authors: Liu Jidong , Ding Guolian , Zou Kexin , Jiang Ziru , Zhang Junyu , Lu Yunhua , Pignata Antonella , Venner Eric , Liu Pengfei , Liu Zhandong , Wangler Michael F. , Sun Zheng 
Published: January 2020

AbstractBackgroundGermline mutations in PTEN are associated with the PTEN hamartoma tumor syndrome (PHTS), an umbrella term used to describe a spectrum of autosomal‐dominant disorders characterized by variable phenotypic manifestations associated with cell or tissue overgrowth. We report a boy who developed severe progressive abdominal distention due to a dramatic adipose mass from the age of 7 months and developed recurrent hypoinsulinemic hypoglycemia that led to seizures at the age of 4 years.MethodsTrio‐based whole‐genome sequencing was performed by using blood DNA from the child and his parents. The possible pathogenic variants were verified by Sanger sequencing. Functional characterization of the identified variant was completed by western blot.ResultsThe child inherited a single‐nucleotide deletion NM_000314.6:c.849delA (p.Glu284Argfs) in the tumor suppressor gene PTEN from his father. The paternal family members have a history of cancer. It is conceivable that PTEN loss‐of‐function induced the adipose tumor growth and hypoglycemia, although the proband did not meet the usual diagnosis criteria of Cowden syndrome or Bannayan–Riley–Ruvalcaba syndrome that are characterized by germline mutations of PTEN.ConclusionThis case underlines the variability of phenotypes associated with PTEN germline mutations and provides useful information for diagnosis and genetic counseling of PTEN‐related diseases for pediatric patients.
A new open‐source GPU‐based microscopic Monte Carlo simulation tool for the calculations of DNA damages caused by ionizing radiation ‐‐‐ Part I: Core algorithm and validation
Authors: Tsai Min‐Yu , Tian Zhen , Qin Nan , Yan Congchong , Lai Youfang , Hung Shih‐Hao , Chi Yujie , Jia Xun 
Published: January 2020

PurposeMonte Carlo (MC) simulation of radiation interactions with water medium at physical, physicochemical, and chemical stages, as well as the computation of biologically relevant quantities such as DNA damages, are of critical importance for the understanding of microscopic basis of radiation effects. Due to the large problem size and many‐body simulation problem in the chemical stage, existing CPU‐based computational packages encounter the problem of low computational efficiency. This paper reports our development on a GPU‐based microscopic Monte Carlo simulation tool gMicroMC using advanced GPU‐acceleration techniques.MethodsgMicroMC simulated electron transport in the physical stage using an interaction‐by‐interaction scheme to calculate the initial events generating radicals in water. After the physicochemical stage, initial positions of all radicals were determined. Simulation of radicals’ diffusion and reactions in the chemical stage was achieved using a step‐by‐step model using GPU‐accelerated parallelization together with a GPU‐enabled box‐sorting algorithm to reduce the computations of searching for interaction pairs and therefore improve efficiency. A multi‐scale DNA model of the whole lymphocyte cell nucleus containing ~6.2 Gbp of DNA was built.ResultsAccuracy of physical stage simulation was demonstrated by computing stopping power and track length. The results agreed with published data and the data produced by GEANT4‐DNA (version 10.3.3) simulations with 10 ‐20% difference in most cases. Difference of yield values of major radiolytic species from GEANT4‐DNA results was within 10%. We computed DNA damages caused by monoenergetic 662 keV photons, approximately representing 137Cs decay. Single‐strand break (SSB) and double‐strand break (DSB) yields were 196 ± 8 SSB/Gy/Gbp and 7.3 ± 0.7 DSB/Gy/Gbp, respectively, which agreed with the result of 188 SSB/Gy/Gbp and 8.4 DSB/Gy/Gbp computed by Hsiao et al. Compared to computation using a single CPU, gMicroMC achieved a speedup factor of ~540x using an NVidia TITAN Xp GPU card.ConclusionsThe achieved accuracy and efficiency demonstrated that gMicroMC can facilitate research on microscopic radiation transport simulation and DNA damage calculation. gMicroMC is an open‐source package available to the research community.
On viscoplastic regularisation of strain‐softening rocks and soils
Authors: de Borst René , Duretz Thibault 
Published: January 2020

SummaryConstitutive models for rocks and soils typically incorporate some form of strain softening. Moreover, many plasticity models for frictional materials use a nonassociated flow rule. Strain softening and nonassociated flow rules can cause loss of well‐posedness of the initial‐value problem, which can lead to a severe mesh dependence in simulations and poor convergence of the iterative solution procedure. The inclusion of viscosity, which is a common property of materials, seems a natural way to restore well‐posedness, but the mathematical properties of a rate‐dependent model, and therefore the effectiveness with respect to the removal of mesh dependence, can depend strongly on how the viscous element is incorporated. Herein, we show that rate‐dependent models, which are commonly applied to problems in the Earth's lithosphere, such as plate tectonics, are very different from the approach typically adopted for more shallow geotechnical engineering problems. We analyse the properties of these models under dynamic loadings, using dispersion analyses and one‐dimensional finite difference analyses, and complement them with two‐dimensional simulations of a typical strain localisation problem under quasi‐static loading conditions. Finally, we point out that a combined model, which features two viscous elements, may be the best way forward for modelling time‐dependent failure processes in the deeper layers of the Earth, since it not only enables modelling of the creep characteristics typical of long‐term behaviour but also regularises the initial/boundary‐value problem.
Readability of pelvic floor dysfunction questionnaires
Authors: Gaines Tyler , Malik Rena D. 
Published: January 2020

AbstractBackgroundThe National Institutes of Health and Center for Disease Control recommend the readability of self‐administered patient questionnaires to be written at or below a sixth to eight grade reading level. The aim of this study is to evaluate the readability of commonly used urinary incontinence (UI), pelvic organ prolapse (POP), overactive bladder (OAB), and benign prostate hyperplasia (BPH) questionnaires.MethodsEighteen validated urologic questionnaires were analyzed using four readability assessment tools. A mean grade‐level needed to comprehend each questionnaire was calculated.ResultsFor UI questionnaires, three out of five questionnaires required a reading level of 10th grade or higher, two grade levels above recommendations. Only one POP questionnaire met recommendations with a mean readability score of 5.9, whereas the other questionnaires required a ninth‐grade reading level or higher. For the OAB questionnaires, three out of five questionnaires met reading recommendations. Readability scores for BPH questionnaires ranged from 6.4 to 11.2, with only the International Prostate Symptom Score questionnaire in compliance with recommendations.ConclusionsThe majority of currently available pelvic floor dysfunction questionnaires do not comply with recommended reading levels, suggesting that these questionnaires are written at a level too advanced for a large proportion of the population. This limits their effectiveness in accurately assessing symptom severity and impact on quality of life.
Basement faults deduction at a dumpsite using advanced analysis of gravity and magnetic anomalies
Authors: Alatorre‐Zamora Miguel Angel , Campos‐Enriquez José Oscar , Fregoso Emilia , Belmonte‐Jiménez Salvador Isidro , Chávez‐Segura René , Gaona‐Mota Marcos 
Published: January 2020

ABSTRACTA study of the fracture systems in the basement of the Matatlan urban waste dump of Guadalajara City, near the western edge of the Rio Grande de Santiago canyon (southwestern Mexico), is reported. The Matatlan dumpsite was developed on top of andesitic and rhyolitic rocks. Measurements at outcrops indicated that N–S (0°–15° and 165°–180°), N45–90E and N105–135E fracture systems affect the basement. Statistical analysis (micromagnetic method) of magnetic lineament azimuths indicated the presence of two lineament groups. The major one (N60–120E) has a maximum at N90–105E, and a secondary group (N120–165E). The gravity anomalies are featured by a major group (N60–120E, with maximums at N60–75E, and N105–120E) and a secondary group (N120–180E). Thus, a good to fair correlation exists between the measured fracture orientations and the lineaments featuring the gravity and magnetic anomalies. Horizontal derivative and tilt angle depicted horizontal limits of anomaly‐causative bodies. Results of the micromagnetic method are consistent with fracture orientations and with the limits established through edge‐detection techniques. Lineaments established by means of the gravity and magnetic Euler deconvolution are also consistent. Gravity and magnetic Euler deconvolution helped to estimate the depth extent of the limits of gravity and magnetic common sources. Euler deconvolution indicated the fault or contact nature of these lineaments. Furthermore, Euler deconvolution indicated slopes of the limits of gravity and magnetic sources. The fault or fracture nature of the major lineaments was finally confirmed by forward modelling (forward 2D cooperative modelling of gravity and magnetic profiles). For example, lineaments delimiting the northern depression could be characterized as normal faults. In general, this study indicates that it is possible, based on gravity and magnetic data, to characterize fractures affecting the basement of a dumpsite, a key parameter in hydrogeophysical studies. In particular, through this study, the inferred structures could be associated with regional tectonic faulting, which might provide migration paths to unhealthy lixiviate outside the dumpsite, giving rise to the contamination of the neighbouring environment. In particular, the study explains the presence of an unhealthy leachate waterfall to the northeast of the dumping site. Heavy metal contents in samples from this waterfall support that lixiviates originate at the dumpsite.
Mitochondrial Pyruvate Carriers are not Required for Adipogenesis but are Regulated by High‐Fat Feeding in Brown Adipose Tissue
Authors: Burrell Jasmine A. , Richard Allison J. , King William T. , Stephens Jacqueline M. 
Published: January 2020

ObjectiveThe objectives of this study were to assess the role of mitochondrial pyruvate carriers (MPCs) in adipocyte development in vitro and determine whether MPCs are regulated in vivo by high‐fat feeding in male and female C57BL/6J mice.MethodsThis study utilized small interfering RNA‐mediated knockdown to assess the requirement of MPC1 for adipogenesis in the 3T3‐L1 model system. Treatment with UK‐5099, a potent pharmacological MPC inhibitor, was also used to assess the loss of MPC activity. Western blot analysis was performed on adipose tissue samples from mice on a low‐fat diet or a high‐fat diet (HFD) for 12 weeks.ResultsThe loss of MPC expression via small interfering RNA‐mediated knockdown or pharmacological inhibition did not affect adipogenesis of 3T3‐L1 cells. In vivo studies indicated that expression of MPCs was significantly decreased in brown adipose tissue of male mice, but not female, on an HFD.ConclusionsAlthough MPCs are essential for pyruvate transport, MPCs are not required for adipogenesis in vitro, suggesting that other substrates can be used for energy production when the MPC complex is not functional. Also, a significant decrease in MPC1 and 2 expression occurred in brown fat, but not white fat, of male mice fed an HFD.
Appetite‐Related Responses to Overfeeding and Longitudinal Weight Change in Obesity‐Prone and Obesity‐Resistant Adults
Authors: Halliday Tanya M. , Rynders Corey A. , Thomas Elizabeth , Bergouignan Audrey , Pan Zhaoxing , Kealey Elizabeth H. , Cornier Marc‐Andre , Bessesen Daniel H. 
Published: January 2020

ObjectiveAppetite responses to 3 days of overfeeding (OF) were examined as correlates of longitudinal weight change in adults classified as obesity prone (OP) or obesity resistant (OR).MethodsOP (n = 22) and OR (n = 30) adults consumed a controlled eucaloric and OF diet (140% of energy needs) for 3 days, followed by 3 days of ad libitum feeding. Hunger and satiety were evaluated by visual analog scales. Ghrelin and peptide YY (PYY) levels were measured during a 24‐hour inpatient visit on day 3. Body weight and composition were measured annually for 4.0 ± 1.3 years.ResultsDietary restraint and disinhibition were greater in OP than OR (mean difference: 3.5 ± 1.2 and 3.3 ± 0.9, respectively; P < 0.01) participants, and disinhibition was associated with longitudinal weight change (n = 48; r = 0.35; P = 0.02). Compared with the eucaloric diet, energy intake fell significantly in OR participants following OF (P = 0.03) but not in OP (P = 0.33) participants. Twenty‐four‐hour PYY area under the curve values increased with OF in OR (P = 0.02) but not in OP (P = 0.17) participants. Furthermore, changes in PYY levels with OF correlated with measured energy intake (r = −0.36; P = 0.01).ConclusionsBaseline disinhibition and PYY responses to OF differed between OP and OR adults. Dietary disinhibition was associated with 5‐year longitudinal weight gain. Differences in appetite regulation may underlie differences in propensity for weight gain.
A comprehensive, self‐contained derivation of the one‐body density matrices from single‐reference excited‐state calculation methods using the equation‐of‐motion formalism
Authors: Etienne Thibaud 
Published: January 2020

AbstractIn this contribution, we review in a rigorous, yet comprehensive fashion the assessment of the one‐body reduced density matrices derived from the most used single‐reference excited‐state calculation methods in the framework of the equation‐of‐motion formalism. Those methods are separated into two types: those which involve the coupling of a deexcitation operator to a single‐excitation transition operator, and those which do not involve such a coupling. The case of many‐body auxiliary wave functions for excited states is also addressed. For each of these approaches we were interested in deriving the elements of the one‐body transition and difference density matrices, and to highlight their particular structure. This has been accomplished by applying a decomposition of integrals involving one‐determinant quantum electronic states on which two or three pairs of second quantization operators can act. Such a decomposition has been done according to a corollary to Wick's theorem, which is brought in a comprehensive and detailed manner. A comment is also given about the consequences of using the equation‐of‐motion formulation in this context, and the two types of excited‐state calculation methods (with and without coupling excitations to deexcitations) are finally compared from the point of view of the structure of their transition and difference density matrices.