Miracle-dz/UniFAR-FTUs huggingface dataset:
Rigidity theory for biomolecules: concepts, software, and applications

The mechanical heterogeneity of biomolecular structures is intimately linked to their diverse biological functions. Applying rigidity theory to biomolecules identifies this heterogeneous composition of flexible and rigid regions, which can aid in the understanding of biomolecular stability and long‐ranged information transfer through biomolecules, and yield valuable information for rational drug design and protein engineering. We review fundamental concepts in rigidity theory, ways to represent biomolecules as constraint networks, and methodological and algorithmic developments for analyzing such networks and linking the results to biomolecular function. Software packages for performing rigidity analyses on biomolecules in an efficient, automated way are described, as are rigidity analyses on biomolecules including the ribosome, viruses, or transmembrane proteins. The analyses address questions of allosteric mechanisms, mutation effects on (thermo‐)stability, protein (un‐)folding, and coarse‐graining of biomolecules. We advocate that the application of rigidity theory to biomolecules has matured in such a way that it could be broadly applied as a computational biophysical method to scrutinize biomolecular function from a structure‐based point of view and to complement approaches focused on biomolecular dynamics. We discuss possibilities to improve constraint network representations and to perform large‐scale and prospective studies. WIREs Comput Mol Sci 2017, 7:e1311. doi: 10.1002/wcms.1311
HEPATOCYTE CO-CULTURE IN ALGINATE HYDROGEL FOR ANTI-CANCER DRUG ANALYSIS

This paper presents the formation of double-layer cellular tumor spheroid for the co-culture of hepatocyte (HepG2 cancer liver cell and LO2 normal liver cell) using alginate hydrogel. With the microfluidic chip, double-layer cellular tumor spheroid can be formed by the hydrogel droplet to mimic the in vivo environment in which the cancer cell is surrounded by normal cell. A microchip with concentration gradient generation and tumor spheroid trapping site is designed for anti-cancer drug analysis.
Closed photobioreactor for microalgae biomass production under indoor growth conditions

As the production of energy and valuable byproducts from microalge requires large quantities of biomass, so it was important to select a cultivation system suitable for large-scale biomass production. Compared with other culturing systems, the tubular closed photobioreactor was the most suitable for good biomass productivity. It appears to hold the greatest promise for monoculture for producing tonnage quantities of the biomass. Three microalgal isolates Chlamydomonas variabilis, Spirulina platensis and Microcystis aeruginosa were cultivated using BG11 media inside 24 tubular vertical glass vessel photobiorector. The biomass productivity of Chlamydomonas variabilis (growth conditions, temperature 25±2oC, pH 7.3-9 and light intensity 1500-3000 lux) reached maximum level in 48hrs (0.03 g dry/L per day ) and incase of Microcystis aeruginosa (growth conditions, temperature 25±2oC, pH 7.3-8 and light intensity 1500-2000 lux) the maximum growth rate reached after 72 hrs (0.7 g dry/L per day) but it took 5 days (0.26 g dry/L per day) with Spirulina platensis (growth conditions, temperature 28±2oC, pH 7.3-8 and light intensity 1500-2000 lux).
Effect of Vibration Foam Rolling and Non-Vibration Foam Rolling in the Lower Extremities on Jump Height

The objective of this study was to investigate whether a vibration stimulus combined with foam rolling yields better power output in the lower extremities during a countermovement jump (CMJ), than a group who uses foam rolling without vibration compared to no warm-up. Eighteen female and male participants, EWU athletes volunteered for this study but three were unable to complete all testing. The design was a randomized cross-over design so all participants served as their own control by participating in all three interventions which consist of; (a) no-warm-up, (b) non-vibration foam rolling (FRNV), and (c) vibration foam rolling (FRV). Post-intervention measurements were compared for differences in anaerobic power assessed by a jump reach test using the Vertc. Each foam rolling session lasted six minutes on each leg with 90 seconds per muscle group. The muscles were foam rolled in a specific order starting with the hamstring, quadriceps gastrocnemius, and soleus. Three countermovement jumps (CMJ) were conducted to achieve maximal height. The highest max CMJ jump was used for data collection. Participants were tested with one day between sessions at the same time each day. A repeated measures ANOVA was calculated to compare the mean scores of no warm-up jump mean to FRNV and FRV jump height scores. No significant effect was found (F(2,28) = . 669, p > . 05) with all subjects included. Though the Shapiro Wilks test indicated a normal distribution, the population was small and the box plots showed three outliers. A second repeated measures ANOVA was then run with outliers removed to determine if significance would occur without extreme scores present, but the results were still non-significant (F(2,22) = 2.152, p > . 05). In conclusion, the present study indicated that performing one and a half minutes of FRNV, FRV compared to no warm-up had a non-significant effect on jump height.
Recovering Trees with Convex Clustering

Convex clustering refers, for given $\left\{x_1, \dots, x_n\right\} \subset \mathbb{R}^p$, to the minimization of \begin{eqnarray*} u(\gamma) & = & \underset{u_1, \dots, u_n }{\arg\min}\;\sum_{i=1}^{n}{\lVert x_i - u_i \rVert^2} + \gamma \sum_{i,j=1}^{n}{w_{ij} \lVert u_i - u_j\rVert},\\ \end{eqnarray*} where $w_{ij} \geq 0$ is an affinity that quantifies the similarity between $x_i$ and $x_j$. We prove that if the affinities $w_{ij}$ reflect a tree structure in the $\left\{x_1, \dots, x_n\right\}$, then the convex clustering solution path reconstructs the tree exactly. The main technical ingredient implies the following combinatorial byproduct: for every set $\left\{x_1, \dots, x_n \right\} \subset \mathbb{R}^p$ of $n \geq 2$ distinct points, there exist at least $n/6$ points with the property that for any of these points $x$ there is a unit vector $v \in \mathbb{R}^p$ such that, when viewed from $x$, `most' points lie in the direction $v$ \begin{eqnarray*} \frac{1}{n-1}\sum_{i=1 \atop x_i \neq x}^{n}{ \left\langle \frac{x_i - x}{\lVert x_i - x \rVert}, v \right\rangle} & \geq & \frac{1}{4}. \end{eqnarray*}
The Elephant Trunk Nebula and the Trumpler 37 cluster: contribution of triggered star formation to the total population of an HII region

Rich young stellar clusters produce Hii regions whose expansion into the nearby molecular cloud is thought to trigger the formation of new stars. However, the importance of this mode of star formation is uncertain. This investigation seeks to quantify triggered star formation (TSF) in IC 1396A (a.k.a., the Elephant Trunk Nebula), a bright rimmed cloud (BRC) on the periphery of the nearby giant Hii region IC 1396 produced by the Trumpler 37 cluster. X-ray selection of young stars from Chandra X-ray Observatory data is combined with existing optical and infrared surveys to give a more complete census of the TSF population. Over 250 young stars in and around IC 1396A are identified; this doubles the previously known population. A spatio-temporal gradient of stars from the IC 1396A cloud toward the primary ionizing star HD 206267 is found. We argue that the TSF mechanism in IC 1396A is the radiation-driven implosion process persisting over several million years. Analysis of the X-ray luminosity and initial mass functions indicates that > 140 stars down to 0.1 M⊙ were formed by TSF. Considering other BRCs in the IC 1396 Hii region, we estimate the TSF contribution for the entire Hii region exceeds 14 25% today, and may be higher over the lifetime of the Hii region. Such triggering on the periphery of Hii regions may be a significant mode of star formation in the Galaxy.
hat’s New in Vascular Surgery

D r V m l r i g p c h c f d t f a l he past year has been one of significant activity in ascular surgery, on the organizational, clinical, and reearch levels. Perhaps the most significant development f the year was the decision by the two major national ascular societies, the Society for Vascular Surgery and he American Association for Vascular Surgery (AAVS), o combine to form one organization with a coordinated trategic plan to enhance development of the specialty of ascular surgery in the future. This effort, which was led y the executive leadership of the two societies, was ratfied by the membership at the conjoined annual meetng in June 2003. The resulting merged society, which ill retain the name of the Society for Vascular Surgery, as moved its executive offices to Chicago in the buildng owned by the American College of Surgeons. This as done to provide a greater focus for the new Society SVS) and to enhance the relationship between vascular urgery and the American College of Surgeons. The newly reorganized SVS will focus on advancing xcellence and innovation in vascular health and reinorcing the position of vascular surgeons as leaders in ascular health care. The SVS has established six critical trategic initiatives for implementation over the next 2 ears: modification and improvement of the current raining paradigm in vascular surgery, enhancement of ducational programs in vascular disease, strengthening ommunication between vascular surgery and governent at all levels, increasing public awareness of vascular isease and the role of vascular surgeons in improving ascular health, improving communications between he vascular surgical community and industry, and erging the foundations of the two organizations. This roactive approach is designed to position the commu-
Using Ambiguous Handwritten Digits to Induce Uncertainty

The lack of ground truth labels is a significant challenge in the field of automatic recognition of emotion and affect. The most common approach to acquiring affect labels is to ask a panel of listeners to rate a corpus of spoken utterances along one or more dimensions of interest. In this paper, we describe a method that uses ambiguous handwritten digits for the purpose of inducing natural uncertainty. Using a crowdsourcing approach, we quantify the legibility of each handwritten digit. These images are integrated into visual stimuli that are used in a lab experiment for eliciting spontaneous spoken utterances of varying levels of certainty. While we cannot measure a speaker’s actual internal level of certainty, our method generates a novel and interesting approximation for internal certainty.
Assessing institutional and environmental parameters of agricultural water use in South Asia: evidences from the Indo-Gangetic Basin

The Indo-Gangetic Basin encompasses most of the fertile landholdings in South Asia. However, low agricultural productivity is observed in the four riparian countries - India, Pakistan, Nepal and Bangladesh - by nailing down rural welfare. Accusations are directed at the inability of water supply sector to ensure high productivity rates and security of subsistence farmers. However, little is known about the demand side and farmers’ perceptions towards the effects of water use on agricultural productivity. To this aim, we conduct an economic assessment through a stated preference approach on crucial institutional and environmental related parameters of agricultural water that could enhance productivity potential. Also, vital socio-demographic elements are examined as influential factors. The analysis is based on an extensive research survey accomplished in selected clusters along the Indo-Gangetic Basin.
Implementing Evolutionary Processors in JAVA: A case study *

Networks of Evolutionary Processors are universal models of computation inspired by point mutations in DNA strands performed in nature. These models have been used to solve NP-complete problems efficiently under a parallel computation assumption. Here, we propose a Java architecture for the Evolutionary Processors of the network as a first step to obtain a full simulator of the model. We propose Java methods and interfaces in order to obtain a versatile and portable version of the model. In order to show our proposal we will study the case of solving a classical problem in computational complexity theory, the well known Satisfiability Problem (SAT).
Ultrathin MoS2/Nitrogen‐Doped Graphene Nanosheets with Highly Reversible Lithium Storage

The extensive range of possibilities for using a rechargeable lithium ion battery (LIB) for stationary power storage applications has stimulated signifi cant research to improve its energy, power density and cycling life. The current use of graphite as a commercially available anode material cannot fully meet the energy density requirements for LIB applications in electric vehicles due to its relatively small capacity (372 mAh/g). In the next generation LIB, graphite should be replaced by alternative higher capacity materials and graphene based composite is one of the promising choices. The discovery of graphene has attracted wide-ranging interest due to its unique physical and chemical properties and potential for applications in electronic devices and sensors. [ 1–3 ] This has led to the development of a signifi cant number of graphene-based materials for use as LIB anodes and results have been generally promising due to high specifi c capacity and improvement of its cycling ability. In recent years, chemical substitutional doping has been used to enhance the properties of graphene—further improving its properties beyond just morphology and size control. This includes the use of sulfur, boron, and nitrogen doping, the latter of which is particularly effective in modulating the electronic properties of graphene. [ 4–6 ] Based on these results, we expect that nitrogen-doped (N-doped) graphene will be used as a template for synthesis of active electrode materials. Compared to graphene-based metal oxide materials, some graphene-based transition metal sulfi des possess consummate 2D-layered structures. The matched structure between transition metal sulfi des and graphene avoids the exfoliation of electrode materials and capacity fading during the charge/discharge process. [ 7–9 ] As a typical layered transition metal sulfi de, MoS 2 has a structure similar to graphite, consisting of three atom layers of S-Mo-S stacked together through van der Waals interactions. [ 10 , 11 ] This layered structure enables the effi cient intercalation and deintercalation of lithium ions. In recent years, many published reports have articulated various processes for preparing MoS 2 or MoS 2 composites as LIB anodes, which
Medicinal Orchids of Nepal: Are They Well Protected?

This paper aims to explore distribution pattern of orchids used for medicinal purpose and their conservation aspect. We compiled information on 82 species of orchids which are used as herbal medicine. Maximum richness of medicinal orchids was observed at an elevation of 1700 msl but, the maximum numbers of protected areas are located at an elevation of 3000 to 3500 msl. There is a negative correlation between number of protected areas and medicinal orchid species richness mentioning that the protected areas are less synchronized with medicinal orchids of Nepal. DOI: 10.3126/on.v8i1. 4315
Towards Teacher-AI Hybrid Systems

AI-powered educational software, such as intelligent tutoring systems (ITSs), is commonly designed to enhance student learning. However, such software is not typically designed to effectively collaborate with human teachers. The present work explores how AI and teachers might leverage and amplify one another’s complementary strengths to achieve outcomes greater than either could achieve alone. Key contributions of this research, so far, include (1) an initial, broad exploration of K-12 teachers’ needs and desires for real-time support in ITS classrooms; (2) the first exploration of the affordances of smart glasses to support orchestration of personalized classrooms, resulting in a prototype called Lumilo; (3) a new prototyping method for real-time teacher support tools; and (4) a classroom experiment evaluating the effects of teacher/AI co-orchestration, supported by Lumilo, on teacher and student behavior and student learning outcomes in classrooms using ITSs.
Mass balance, flow and subglacial processes of a modelled Younger Dryas ice cap in Scotland

Abstract We use an empirically validated high-resolution three-dimensional ice-sheet model to investigate the mass-balance regime, flow mechanisms and subglacial characteristics of a simulated Younger Dryas Stadial ice cap in Scotland, and compare the resulting model forecasts with geological evidence. Input data for the model are basal topography, a temperature forcing derived from GRIP δ18O fluctuations and a precipitation distribution interpolated from modern data. The model employs a positive-degree-day scheme to calculate net mass balance within a domain of 112500 km2, which, under the imposed climate, gives rise to an elongate ice cap along the axis of the western Scottish Highlands. At its maximum, the ice cap is dynamically and thermally zoned, reflecting topographic and climatic controls, respectively. In order to link these palaeoglaciological conditions to geological interpretations, we calculate the relative balance between sliding and creep within the simulated ice cap, forecast areas of the ice cap with the greatest capacity for basal erosion and predict the likely pattern of subglacial drainage. We conclude that ice flow in central areas of the ice cap is largely due to internal deformation, and is associated with geological evidence of landscape preservation. Conversely, the distribution of streamlined landforms is linked to faster-flowing ice whose velocity is predominantly the result of basal sliding. The geometry of the main ice mass focuses subglacial erosion in the mid-sections of topographic troughs, and produces glaciohydraulic gradients that favour subglacial drainage through low-order arterial routes.
Chapter 3 from: LOCAL MOTION DETECTION: COMPARISON OF HUMAN AND MODEL OBSERVERS A Dissertation for the Department of Neuroscience at the University of Pennsylvania

Since the first filter based models of local motion detection were introduced [38, 35, 1], the idea that the visual system uses a set of spatio-temporal bandpass filters to analyze visual motion information has gained a great deal of support (e.g. [1, 4, 8, 6, 5, 3, 13, 33, 21, 22, 39]). What characterizes these filters is that their frequency selectivity is concentrated around a single spatio-temporal frequency [34]. Several interesting kinds of retinal motion can be encoded by selectively pooling the outputs of these filters, and virtually every motion processing model can be expressed in terms of the outputs of these filters [28]. For instance, the velocity of a translating pattern can be encoded by pooling the filters whose peak frequencies lie in a common plane [34, 14, 12, 28], ’opponent’ motion by subtractively pooling filters tuned for opposite directions [29], ’group velocity’ by pooling along contours orthogonal to a plane through the origin [10], and gradients in the motion field can be detected by subtractively pooling estimates of retinal velocity across adjacent spatial regions of the retina [37]. In addition, a large class of phenomena have been modeled by allowing nonlinear interactions between the outputs of spatio-temporal filters, including contrast normalization [20, 15], motion induction [24, 18], motion contrast [16], motion transparency [25], and trajectory detection [31], among others. Each type of filter output pooling corresponds to a strategy for encoding information which is optimal for a certain task. For instance, planar pooling is optimal for detecting translations and ’opponent motion’ pooling for discriminating opposite moving gratings. The results of the experiments in chapter 2 (particularly for ’Scrambled’ stimuli) showed that subjects are not able to adopt arbitrary detection strategies. Thus the pooling strategies used by the visual system tell us something about the tasks the visual system is optimized to perform. In this chapter we examine two related issues: What pooling strategies do subjects use in detecting local motions, and How adaptable are the visual system’s pooling strategies to the demands of a task? We investigate these questions by focusing on how the visual system combines frequency information to detect four different stimulus types: the Planar, Scrambled, and Component stimuli used in chapter 2, plus one new stimulus type described below. Optimal detection performance on each stimulus type requires a qualitatively different pooling strategy. We perform a kind of perturbation analysis on the detection data which allows us to infer how subjects weight a set of frequency bands when detecting the stimuli. The analysis we used is similar to several
Impact of the Query Set on the Evaluation of Expert Finding Systems

Expertise is a loosely defined concept that is hard to formalize. Much research has focused on designing efficient algorithms for expert finding in large databases in various application domains. The evaluation of such recommender systems lies most of the time on human-annotated sets of experts associated with topics. The protocol of evaluation consists in using the namings or short descriptions of these topics as raw queries in order to rank the available set of candidates. Several measures taken from the field of information retrieval are then applied to rate the rankings of candidates against the ground truth set of experts. In this paper, we apply this topic-query evaluation methodology with the AMiner data and explore a new document-query methodology to evaluate experts retrieval from a set of queries sampled directly from the experts documents. Specifically, we describe two datasets extracted from AMiner, three baseline algorithms from the literature based on several document representations and provide experiment results to show that using a wide range of more realistic queries provides different evaluation results to the usual topic-queries.
Sex-Dependent Variation of Pumpkin (Cucurbita maxima cv. Big Max) Nectar and Nectaries as Determined by Proteomics and Metabolomics

Nectar is a floral reward that sustains mutualisms with pollinators, which in turn, improves fruit set. While it is known that nectar is a chemically complex solution, extensive identification and quantification of this complexity has been lacking. Cucurbita maxima cv. Big Max, like many cucurbits, is monoecious with separate male and female flowers. Attraction of bees to the flowers through the reward of nectar is essential for reproductive success in this economically valuable crop. In this study, the sex-dependent variation in composition of male and female nectar and the nectaries were defined using a combination of GC-MS based metabolomics and LC-MS/MS based proteomics. Metabolomics analysis of nectar detected 88 metabolites, of which 40 were positively identified, and includes sugars, sugar alcohols, aromatics, diols, organic acids, and amino acids. There are differences in 29 metabolites between male and female nectar. The nectar proteome consists of 45 proteins, of which 70% overlap between nectar types. Only two proteins are unique to female nectar, and 10 are specific to male nectar. The nectary proteome data, accessible at ProteomeXchange with identifier PXD009810, contained 339 identifiable proteins, 71% of which were descriptively annotatable by homology to Plantae. The abundance of 45 proteins differs significantly between male and female nectaries, as determined by iTRAQ labeling. This rich dataset significantly expands the known complexity of nectar composition, supports the hypothesis of H+-driven nectar solute export, and provides genetic and chemical targets to understand plant–pollinator interactions.