Miracle-dz/UniFAR-FTUs huggingface dataset:
A Python Script to Compute Isochrones for MODFLOW

MODFLOW constitutes today the most popular modeling tool in the study of water flow in aquifers and in modeling aquifers. To simplify the interface to MODFLOW various GUI have been developed for the creation of model definition files and for the visualization and interpretation of results. Recently Bakker et al. (2016) developed the FloPy interface to MODFLOW that allows to import and use the produced simulation data using Python. This allows to construct model input files, run the models, read and plot simulations results through Python scripts. In this note, we present a Python program (that uses FloPy) interface that allows us to generate time‐related capture zones (isochrones) for confined 2D steady‐state groundwater flow in unbounded domains, with one or more wells. As an application, we show a validation of the approach and the results of four basic test cases: a homogenous aquifer with one well, a heterogeneous aquifer with one well, an aquifer with four wells located both longitudinal and perpendicular to the flow direction.
Deep Learning-Based Channel Estimation for Beamspace mmWave Massive MIMO Systems

Channel estimation is very challenging when the receiver is equipped with a limited number of radio-frequency (RF) chains in beamspace millimeter-wave massive multiple-input and multiple-output systems. To solve this problem, we exploit a learned denoising-based approximate message passing (LDAMP) network. This neural network can learn channel structure and estimate channel from a large number of training data. Furthermore, we provide an analytical framework on the asymptotic performance of the channel estimator. Based on our analysis and simulation results, the LDAMP neural network significantly outperforms state-of-the-art compressed sensing-based algorithms even when the receiver is equipped with a small number of RF chains.
The effect of adding cholesterol to laying hen diets as powder or predissolved in fat.

An experiment was conducted to determine if adding supplemental cholesterol to the feed or first adding it to the supplemental fat source of laying hen diets would result in differences in egg yolk and liver cholesterol levels. Five levels of cholesterol (0, .5, 1, 2, and 4%) and three levels of animal tallow (0, 4, and 8%) were used. The diets were randomly assigned and fed for 35 days to individually caged hens within each of six replicates. Eggs laid on or near Days 0, 7, 14, 21, 28, and 35 were used for cholesterol analysis. Liver cholesterol, egg production, and feed intake were also assessed. Mixing cholesterol with the fat source before feed incorporation did not promote higher yolk or liver cholesterol levels and were essentially the same as the method in which powdered cholesterol was added directly to the feed. A linear increase in yolk and liver cholesterol was observed with 0, . 5, and 1% dietary cholesterol. Yolk cholesterol also increased linearly during the first 14 days of cholesterol administration. Further increases in yolk cholesterol, however, were not obtained with either the higher levels of dietary cholesterol or the extended feeding times.
Investigation of Parent Austenite Grains from Martensite Structure Using EBSD in a Wear Resistant Steel

Crystallographic reconstruction of parent austenite grain boundaries from the martensitic microstructure in a wear resistant steel was carried out using electron backscattered diffraction (EBSD). The present study mainly aims to investigate the parent austenite grains from the martensitic structure in an as-rolled (reference) steel sample and samples obtained by quenching at different cooling rates with corresponding dilatometry. Subsequently, this study is to correlate the nearest cooling rate by the dilatometer which yields a similar orientation relationship and substructure as the reference sample. The Kurdjumov-Sachs orientation relationship was used to reconstruct the parent austenite grain boundaries from the martensite boundaries in both reference and dilatometric samples using EBSD crystallographic data. The parent austenite grain boundaries were successfully evaluated from the EBSD data and the corresponding grain sizes were measured. The parent austenite grain boundaries of the reference sample match the sample quenched at 100 °C/s (CR100). Also the martensite substructures and crystallographic textures are similar in these two samples. The results from hardness measurements show that the reference sample exhibits higher hardness than the CR100 sample due to the presence of carbides in the reference sample.
As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy

Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom (AA) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein (HA-Gō), the associative memory, water mediated, structure and energy model (AWSEM) which has 3 interaction sites per amino acid, and a Gō model containing only one interaction site per amino acid at the Cα position (Cα-Gō). To systematically compare results across models, the scales of time, energy, and force had to be suitably renormalized in each model. Surprisingly, the HA-Gō model gives the softest protein, exhibiting much smaller force peaks than all other models after the above renormalization. Clustering to render a structural taxonomy as the protein unfolds showed that the AA, HA-Gō, and Cα-Gō models exhibit a single pathway for early unfolding, which eventually bifurcates repeatedly to multiple branches only after the protein is about half-unfolded. The AWSEM model shows a single dominant unfolding pathway over the whole range of unfolding, in contrast to all other models. TM alignment, clustering analysis, and native contact maps show that the AWSEM pathway has however the most structural similarity to the AA model at high nativeness, but the least structural similarity to the AA model at low nativeness. In comparison to the AA model, the sequence of native contact breakage is best predicted by the HA-Gō model. All models consistently predict a similar unfolding mechanism for early force-induced unfolding events, but diverge in their predictions for late stage unfolding events when the protein is more significantly disordered.
Effects of High and Low Molecular Weight Chitosan on Plasma Cholesterol, Glucose and Adipocytokines in Diabetic Rats Induced by Streptozotocin and Nicotinamide

Chitosan is known for its lipid-lowering effect. To investigate the comparative effects of low (LCS) and high molecular weight chitosan (HCS) on plasma glucose, cholesterol and adipocytokines, male Sprague-Dawley rats were divided into four groups: normal control, diabetic, and diabetic fed the HCS or LCS diet for seven weeks. Diabetes was induced by subcutaneous injection of nicotinamide and streptozotocin. Results showed that diabetic rats fed the HCS diet had reduced liver weight and perirenal adipose weight, compared to those that were fed the control diet. Higher fecal triglyceride and cholesterol excretion and lower hepatic cholesterol and triglyceride contents were found in diabetic rats fed with both chitosan diets. These observations were more significant in the HCS group than in the LCS group. HCS, but not LCS diet, significantly reduced plasma fructosamine, leptin, total cholesterol and lowered the insulin resistance index (homeostasis model assessment; HOMA) in diabetic rats. A lower intestinal dissaccharidase activity including sucrase and lactase was found in diabetic rats fed the HCS dict. Moreover, plasma tumor necrosis factor-alpha and plasminogen activator inhibitor-1 concentrations were significantly reduced by both chitosan supplementations. The results suggested that HCS feeding may reduce insulin resistance by the suppression of lipid accumulation in liver and adipose tissue and amelioration of chronic inflammation in diabetic rats. HCS may improve glucose and lipid metabolism more significantly than LCS in diabetic rats.
Application of SiO2 Nanoparticles as Lubricant Additive in VCRS: An Experimental Investigation

In this work, the SiO2 nano-oil is proposed as a promising lubricant to enhance the performance of vapour compression refrigerator compressor. The stability of SiO2 nanoparticles in the oil is investigated experimentally. It was confirmed that the nanoparticles steadily suspended in the mineral oil at a stationary condition for long period of time. The application of the nano-oil with specific concentrations of 1%, 2% and 2.5 %( by mass fraction) were added in the compressor oil. The VCRS performance with the nanoparticles was then investigated using energy consumption tests. The result shows the COP of system were improved by 7.61%,14.05% & 11.90%, respectively, when the nano-oil was used instead of pure oil.
Trends in single women with malignancy of the uterine cervix in United States

Objective To examine trends and characteristics of single women with malignancy of the uterine cervix. Methods This is a retrospective observational study examining the United States population-based tumor registry (the Surveillance, Epidemiology, and End Results program). Time-specific trends in single marital status were examined in 3,294,208 women among 12 common female malignancies including 87,151 women with uterine cervical malignancy between 1973 and 2013. Results While the proportion of single women in the majority of malignancies increased during the study time, the proportion of single women with cervical malignancy significantly increased more than in other malignancies (29.3% in 2013 from 6.3% in 1973). There was a surge in the proportion of single women with cervical malignancy starting in the early 1990s, exhibiting the largest annual percentage rate change (APC) among all examined malignancies (1.8%; 95% confidence interval [CI]=1.6, 2.0; p<0.001). There was a significant decrease in the proportion of women aged <40 years with cervical malignancy between 1989 and 2013 (APC, −1.2%; 95% CI=−1.4, −1.0; p<0.001). However, when stratified by age, the proportion of single women aged ≥40 years increased significantly during the time (APC, 2.7%; 95% CI=2.3, 3.2; p<0.001) but did not in those who were <40 years (APC, 0.1%; 95% CI=−0.7, 0.6; p=0.850). Conclusion The proportion of single women with malignancy of the uterine cervix has significantly increased in the past 4 decades. This increase was most dramatic in single women aged ≥40 years. Improving screening strategies in single women aged ≥40 years may help reduce the incidence of this malignancy.
Germ-layer commitment and axis formation in sea anemone embryonic cell aggregates

Significance Embryonic development of any animal species is a robust series of morphogenetic events tightly controlled by molecular signals. However, the variety of developmental trajectories undertaken by different members of the same phylum suggests that normal development in each particular species might involve only a subset of morphogenetic capacities available to the highly developmentally plastic embryonic cells. Here we show that, faced by a new developmental context, the aggregates of dissociated gastrula cells of the sea anemone Nematostella vectensis use an alternative developmental trajectory typical for other, distantly related members of the cnidarian phylum. We conclude that new modes of development may evolve relatively easily due to the versatility and developmental plasticity of embryonic cells. Robust morphogenetic events are pivotal for animal embryogenesis. However, comparison of the modes of development of different members of a phylum suggests that the spectrum of developmental trajectories accessible for a species might be far broader than can be concluded from the observation of normal development. Here, by using a combination of microsurgery and transgenic reporter gene expression, we show that, facing a new developmental context, the aggregates of dissociated embryonic cells of the sea anemone Nematostella vectensis take an alternative developmental trajectory. The self-organizing aggregates rely on Wnt signals produced by the cells of the original blastopore lip organizer to form body axes but employ morphogenetic events typical for normal development of distantly related cnidarians to re-establish the germ layers. The reaggregated cells show enormous plasticity including the capacity of the ectodermal cells to convert into endoderm. Our results suggest that new developmental trajectories may evolve relatively easily when highly plastic embryonic cells face new constraints.
A Dynamic Speech Comprehension Test for Assessing Real-World Listening Ability.

BACKGROUND Many listeners with hearing loss report particular difficulties with multitalker communication situations, but these difficulties are not well predicted using current clinical and laboratory assessment tools. PURPOSE The overall aim of this work is to create new speech tests that capture key aspects of multitalker communication situations and ultimately provide better predictions of real-world communication abilities and the effect of hearing aids. RESEARCH DESIGN A test of ongoing speech comprehension introduced previously was extended to include naturalistic conversations between multiple talkers as targets, and a reverberant background environment containing competing conversations. In this article, we describe the development of this test and present a validation study. STUDY SAMPLE Thirty listeners with normal hearing participated in this study. DATA COLLECTION AND ANALYSIS Speech comprehension was measured for one-, two-, and three-talker passages at three different signal-to-noise ratios (SNRs), and working memory ability was measured using the reading span test. Analyses were conducted to examine passage equivalence, learning effects, and test-retest reliability, and to characterize the effects of number of talkers and SNR. RESULTS Although we observed differences in difficulty across passages, it was possible to group the passages into four equivalent sets. Using this grouping, we achieved good test-retest reliability and observed no significant learning effects. Comprehension performance was sensitive to the SNR but did not decrease as the number of talkers increased. Individual performance showed associations with age and reading span score. CONCLUSIONS This new dynamic speech comprehension test appears to be valid and suitable for experimental purposes. Further work will explore its utility as a tool for predicting real-world communication ability and hearing aid benefit.
Manipulation of the sodium‐potassium ratio as a lever for controlling cell growth and improving cell specific productivity in perfusion CHO cell cultures

Perfusion processes typically require removal of a continuous or semi‐continuous volume of cell culture in order to maintain a desired target cell density. For fast growing cell lines, the product loss from this stream can be upwards of 35%, significantly reducing the overall process yield. As volume removed is directly proportional to cell growth, the ability to modulate growth during perfusion cell culture production thus becomes crucial. Leveraging existing media components to achieve such control without introducing additional supplements is most desirable because it decreases process complexity and eliminates safety and clearance concerns. Here, the impact of extracellular concentrations of sodium (Na) and potassium (K) on cell growth and productivity is explored. High throughput small‐scale models of perfusion revealed Na:K ratios below 1 can significantly suppress cell growth by inducing cell cycle arrest in the G0/1 phase. A concomitant increase in cell specific productivity was also observed, reaching as high as 115 pg/cell/day for one cell line studied. Multiple recombinant Chinese hamster ovary (CHO) cell lines demonstrated similar responses to lower Na:K media, indicating the universal applicability of such an approach. Product quality attributes were also assessed and revealed that effects were cell line specific, and can be acceptable or manageable depending on the phase of the drug development. Drastically altering Na and K levels in perfusion media as a lever to impact cell growth and productivity is proposed.
Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches

Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method.
Host lignin composition affects haustorium induction in the parasitic plants Phtheirospermum japonicum and Striga hermonthica.

Parasitic plants in the family Orobanchaceae are destructive weeds of agriculture worldwide. The haustorium, an essential parasitic organ used by these plants to penetrate host tissues, is induced by host-derived phenolic compounds called haustorium-inducing factors (HIFs). The origin of HIFs remains unknown, although the structures of lignin monomers resemble that of HIFs. Lignin is a natural phenylpropanoid polymer, commonly found in secondary cell walls of vascular plants. We therefore investigated the possibility that HIFs are derived from host lignin. Various lignin-related phenolics, quinones and lignin polymers, together with nonhost and host plants that have different lignin compositions, were tested for their haustorium-inducing activity in two Orobanchaceae species, a facultative parasite, Phtheirospermum japonicum, and an obligate parasite, Striga hermonthica. Lignin-related compounds induced haustoria in P. japonicum and S. hermonthica with different specificities. High concentrations of lignin polymers induced haustorium formation. Treatment with laccase, a lignin degradation enzyme, promoted haustorium formation at low concentrations. The distinct lignin compositions of the host and nonhost plants affected haustorium induction, correlating with the response of the different parasitic plants to specific types of lignin-related compounds. Our study provides valuable insights into the important roles of lignin biosynthesis and degradation in the production of HIFs.
A novel PDWC‐UCO algorithm‐based buffer placement in FPGA architecture

Clock distribution networks consume a significant amount of the whole chip power budget. Therefore, reduction in the power consumption of the clock networks is a significant objective in high‐performance Integrated Circuit (IC) designs. This paper presents a novel Particle Distance Weighted Clustering (PDWC)‐Unity Clustering Optimization (UCO) algorithm for the placement of clock buffers in the Field Programmable Gate Array (FPGA) architecture. A novel PDWC algorithm is applied for clustering the logical components based on the minimum distance between components. A UCO algorithm is developed to determine the location for the placement of the buffers. This clustering technique reduces the delay rate of the architecture because of the minimum number of logical components. The overall area and power consumption of the FPGA architecture are reduced because of the placement of the buffers and latches. Our proposed PDWC‐UCO algorithm achieves lower delay, power consumption, wire length, latency and skew than the existing Flip‐Flop (FF) merging and register clustering algorithms. Copyright © 2016 John Wiley & Sons, Ltd.
Functional Changes after Recombinant Human Growth Hormone Replacement in Patients with Chronic Traumatic Brain Injury and Abnormal Growth Hormone Secretion.

We explored the effects of recombinant human growth hormone (rhGH) replacement on physical and cognitive functioning in subjects with a moderate-to-severe traumatic brain injury (TBI) with abnormal growth hormone (GH) secretion. Fifteen individuals who sustained a TBI at least 12 months prior to study enrollment were identified as having abnormal GH secretion by glucagon stimulation testing (maximum GH response less than 8 ng/mL). Peak cardiorespiratory capacity, body composition, and muscle force testing were assessed at baseline and one year after rhGH replacement. Additionally, standardized neuropsychological tests that assess memory, processing speed, and cognitive flexibility, as well as self-report inventories related to depression and fatigue, were administered at baseline and 1 year after rhGH replacement. Comparison tests were performed with proper post hoc analyses. All analyses were carried out at α < 0.05. Peak O2 consumption, peak oxygen pulse (estimate of cardiac stroke volume), and peak ventilation all significantly increased (p < 0.05). Maximal isometric and isokinetic force production were not altered. Skeletal muscle fatigue did not change but the perceptual rating of fatigue was reduced by ∼25% (p = 0.06). Cognitive performance did not change significantly over time, whereas self-reported symptoms related to depression and fatigue significantly improved. The observed changes suggest that rhGH replacement has a positive impact on cardiorespiratory fitness and a positive impact on perceptual fatigue in survivors of TBI with altered GH secretion.