Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins

Integral and interacting membrane proteins (IIMPs) constitute a vast family of biomolecules that perform essential functions in all forms of life. However, characterizing their interactions with lipid bilayers remains limited due to challenges in purifying and reconstituting IIMPs in vitro or labeling IIMPs without disrupting their function in vivo. Here, we report TXTL-QCMD to dynamically characterize interactions between diverse IIMPs and membranes without protein purification or labeling. As part of TXTL-QCMD, IIMPs are synthesized using cell-free transcription-translation (TXTL), and their interactions with supported lipid bilayers are measured using a quartz crystal microbalance with dissipation (QCMD). TXTL-QCMD reconstitutes known IIMP-membrane dependencies, including specific association with prokaryotic or eukaryotic membranes or oscillating interactions by the E. coli Min system. Applying TXTL-QCMD to the recently discovered Zorya anti-phage system unamenable to labeling, we discovered that ZorA and ZorB integrate together within the lipids found at the poles of bacteria while ZorE diffuses freely on the non-pole membrane. These efforts establish the potential of TXTL-QCMD to broadly characterize the large diversity of IIMPs.
Neutral speciation in realistic populations

de Aguiar et al. have shown that basic patterns of species diversity found in nature can be described by a simple neutral model of speciation in which species emerge as a consequence of local mating and mate preference for genetic similarity. Their results have been cited as support for the neutral theory of biodiversity. However, because the mutation rates considered in their work are much larger than those experienced by living organisms, there is still some question as to whether speciation will occur in the neutral model under realistic conditions. Here, I develop a variant of the neutral model that includes a realistic mechanism for organism dispersal. I explore speciation in the model for a class of mobile organisms (butterflies), and I find that speciation does occur under conditions consistent with butterfly populations, albeit on narrow landscapes. The model also appears to exhibit scaling behavior – specifically, if the model is “scaled up” by increasing the area of the landscape while holding its length to width ratio and population density constant, the number of species tends to an asymptotic value. The results suggest that it is possible to infer speciation patterns in large populations by simulating much smaller, computationally tractable populations.
Discriminative histone imputation using chromatin accessibility

Motivation Histone modifications (HMs) play a crucial role in various biological processes, including transcription, replication, and DNA repair, and they have a significant impact on chromatin structure. However, annotating HMs across different cell types using experimental approaches alone is impractical due to cost and time constraints. Therefore, computational techniques are valuable for predicting HMs, complementing experimental methods, and enhancing our understanding of DNA characteristics and gene expression patterns. Results In this study, we introduce a deep learning model called discriminative histone imputation using chromatin accessibility (dHICA). dHICA combines extensive DNA sequence information with chromatin accessibility data, utilizing the Transformer architecture. This allows dHICA to have a large receptive field, and more cell-type specific information, which can not only incorporate distal information across the entire genome, but also improve predictive accuracy and interpretability. Comparing performance with other models, we found that dHICA exhibits superior performance in both peak calling and signal predictions, especially in biologically salient regions such as gene elements. dHICA serves as a crucial tool for advancing our understanding of chromatin dynamics, offering enhanced predictive capabilities and interpretability, particularly in critical biological regions such as gene elements. Availability and implementation https://github.com/wzhy2000/dHICA and https://dreg.dnasequence. org/. Contact zhongwang@dlut.edu. cn.
ArborSim: Articulated, branching, OpenSim routing for constructing models of multi-jointed appendages with complex muscle-tendon architecture

Computational models of musculoskeletal systems are essential tools for understanding how muscles, tendons, bones, and actuation signals generate motion. In particular, the OpenSim family of models has facilitated a wide range of studies on diverse human motions, clinical studies of gait, and even non-human locomotion. However, biological structures with many joints, such as fingers, necks, tails, and spines, have been a longstanding challenge to the OpenSim modeling community, especially because these structures comprise numerous bones and are frequently actuated by extrinsic muscles that span multiple joints—often more than three—and act through a complex network of branching tendons. Existing model building software, typically optimized for limb structures, makes it difficult to build OpenSim models that accurately reflect these intricacies. Here, we introduce ArborSim, customized software that efficiently creates musculoskeletal models of highly jointed structures and can build branched muscle-tendon architectures. We used ArborSim to construct toy models of articulated structures to determine which morphological features make a structure most sensitive to branching. By comparing the joint kinematics of models constructed with branched and parallel muscle-tendon units, we found that the number of tendon branches and the number of joints between branches are most sensitive to branching modeling method—notably, the differences between these models showed no predictable pattern with increased complexity. As the proportion of muscle increased, the kinematic differences between branched and parallel models units also increased. Our findings suggest that stress and strain interactions between distal tendon branches and proximal tendon and muscle greatly affect the overall kinematics of a musculoskeletal system. By incorporating complex muscle-tendon branching into OpenSim models using ArborSim, we can gain deeper insight into the interactions between the axial and appendicular skeleton, model the evolution and function of diverse animal tails, and understand the mechanics of more complex motions and tasks.
Investigating the molecular basis of cleptobiosis in eusocial stingless bees (Apidae: Hymenoptera)

Cleptobiosis is a widespread strategy among animals in which members of one species raid for food or other valuable resources that were obtained by another species. Obligate cleptobiotic species are however rare, and the eusocial stingless bee Lestrimelitta limao features amongst these rare species. This bee pillages other stingless bee colonies. To provide some insights into the molecular basis and evolution of cleptobiosis in eusocial bees, here we compare transcriptomic data of foraging workers of the robber bee L. limao and three non-robber stingless bees: Nannotrigona testaceicornis, Scaptotrigona depilis, and Tetragonisca angustula. Our findings demonstrate that most of the orthologs identified as differentially expressed (DE) among the robber and the non-robber bees are downregulated in L. limao workers, showing a reduced expression activity in the cleptobiont during foraging. Several DE orthologs potentially regulate neuronal and synaptic activities in addition to other critical cellular functions. Additionally, differentially expressed orthologs associated with floral resource exploration and energetic metabolism were identified. These genes warrant further investigation to enhance our understanding of the specific molecular adaptations associated with cleptobiosis in eusocial terms.
Modelling biological and resource fluxes in fluvial meta-ecosystems

Meta-ecosystem theory predicts that cross-ecosystem flows of energy, nutrients, and organisms have important implications for local community assembly and ecosystem functioning. Developments in the theory also have the potential to enhance our under-standing of biodiversity-ecosystem functioning relationships. Meta-ecosystem theory is particularly well-suited to the study of rivers, because water flow forces strong spatial interrelationships among connected ecosystems. However, models that address flows of both resources and organisms and explicitly link both are lacking. We present a model and associated R-package for cross-ecosystem flows of both resources and organisms that can be used to predict their distribution in river networks, as well as meta-ecosystem functioning. The model incorporates feedbacks between these two crucial components. To illustrate the capabilities of the model, we present an in silico experiment and analysis, as well as providing sample code.
The Life Cycles of Destination Life Cycle Models: A Critical Comparison and Synthesis in the Context of Destinations in Asia

Product Life Cycle (PLC) has always been a hot topic in the tourism literature. Butler’s Tourism Area Lifecycle model and Plog’s destination life cycle model have both been applied and analysed extensively in tourism destination development and lifecycle studies. This study attempts to offer a critical conversation on the similarities and differences as well as the strengths and weaknesses of these two widely referred generic models of destination life cycle. It also identifies some recent socio-political, economic, and technological developments that have changed the nature of tourism destination development in many parts of the world and in particular to Asia and the implications of these developments upon life cycles. Based on more recent research, the present authors suggest that the reality of destination development lies somewhere in between, as a resultant of interaction with the processes laid out by Plog and Butler.
Learning analytics tells: Know your basics and go to class

Research on conceptual modeling education and learning analytics often lacks grounding in instructional design theories. Furthermore, the analysis of blended courses often neglects data about offline activities. This paper investigates the data of one conceptual modeling course the design of which is grounded on Bloom’s taxonomy and the 4C/ID model, and for which intent to participate in on-campus lab sessions was tracked. The results demonstrate that attending the on-campus lab sessions have high predictive value for study success. In addition, using Bloom’s cognitive levels confirms the value of organising assessment along these cognitive levels and offers perspectives for more efficient evaluation of conceptual modeling skills.
Localized Island Model Genetic Algorithm in Population Diversity Preservation

Premature convergence in island model is a consequence of the selection in migration mechanism. It is a process of migrating several individuals (usually the best one) from a source into destination island to keep its diversity. The main reason is the similar characteristic of relocated individual because of the genetic operator configurations are similar. Localized Island Model GA (LIMGA) tries to implement different island characteristics (localization strategy) to preserve the islands’ diversity. By harmonizing standard GA, pseudo GA, and informed GA; LIMGA could overcome general optimization problem with a great result and acceptable execution time. Moreover, because of its success in maintaining the diversity, LIMGA could lead the current best-known-so-far solver for this case. Keywords—migration policy, island model, genetic algorithm, localization strategy
A Cable-Mapping Algorithm Based on Ground-Penetrating Radar

The demand for mapping the buried cables is increasing dramatically with the rapid expansion of urban area, but there are few specific procedures and approaches to map underground cables without disturbing the normal electricity supply. In this letter, a cable-mapping approach based on the ground-penetrating radar (GPR) is proposed, which consists of two parts. First, the parallel scan lines are established along which the GPR is moved to obtain the B-scan images; the hyperbolic shapes on these obtained images are identified and fitted; and the locations and depths of the detected sample points of the buried cables could be derived from these hyperbolas. Then, due to different terrain and surrounding obstacles, as well as the use of pipe-jacking technology,1 the underground cables may not be straight. The detected points are interpolated by a three-dimensional spline interpolation algorithm to obtain a smooth 3-D curve with location and depth information. Compared with the 2-D model, the 3-D curve could visualize the direction of buried cables more intuitively. Also, in comparison with other interpolation algorithms, the error caused by the proposed interpolation is minimized on the chosen data sets. Experiments on real-world data sets are conducted, and the obtained results demonstrate the effectiveness of the proposed model.1Pipe-jacking is a trenchless technology for buried utilities [1].
Human activity recognition using conditional random fields and privileged information

Michalis S. Vrigkas. PhD, Department of Computer Science & Engineering, University of Ioannina, Greece. February, 2016. Thesis Title: Human activity recognition using conditional random fields and privileged information. Thesis Supervisor: Christophoros Nikou. Recognizing human activities from video sequences or still images is a challenging task due to problems such as background clutter, partial occlusion, changes in scale, viewpoint, lighting, and appearance. Many applications, including video surveillance systems, human-computer interaction, and robotics for human behavior characterization, require a multiple activity recognition system. In the first part of this thesis, after a review of the state-of-the-art methods, a learningbased framework for action representation and recognition relying on time series of optical flow motion features is presented. In the learning step, the motion curves representing each action are clustered using Gaussian mixture modeling (GMM). In the recognition step, the optical flow curves of a probe sequence are also clustered using a GMM, then each probe sequence is projected onto the training space and the probe curves are matched to the learned curves using a non-metric similarity function based on the longest common subsequence, which is robust to noise and provides an intuitive notion of similarity between curves. Next, a human behavior recognition method with an application to political speech videos is presented. The behavior of a subject is modeled using a conditional random field (CRF). To evaluate the performance of the model, a novel behavior dataset is introduced, which includes low resolution video sequences depicting different people speaking in the Greek parliament. The subjects of the Parliament dataset are labeled as friendly, aggressive or neutral depending on the intensity of their political speech. An extension of the aforementioned human behavior recognition method using multimodal features is also presented. Individual and social behaviors of a subject are modeled using a hidden conditional random field (HCRF). Each video is represented by a vector of spatio-temporal visual features along with audio features. To remove irrelevant features a feature pruning method based on the spatio-temporal neighborhood of each feature in a video sequence is presented. The proposed framework assumes that human movements are highly correlated with sound emissions and canonical correlation analysis is employed
ε -ISOMETRIC DIMENSION REDUCTION FOR INCOMPRESSIBLE SUBSETS OF (cid:96) P

Fix p ∈ [1 , ∞ ), K ∈ (0 , ∞ ) and a probability measure µ . We prove that for every n ∈ N , ε ∈ (0 , 1) and x 1 ,. ,x n ∈ L p ( µ ) with (cid:13)(cid:13)(cid:13) max i ∈{ 1 ,. ,n } | x i | (cid:13)(cid:13)(cid:13) L p ( µ ) ≤ K , there exists d ≤ 32 e 2 (2 K ) 2 p log n ε 2 and vectors y 1 ,. ,y n ∈ (cid:96) dp such that
Magnetic Field Enhancements in the Interplanetary Solar Wind: Diverse Processes Manifesting a Uniform Observation Type?

17 Within the solar wind throughout the inner heliosphere, observations reveal the presence 18 of magnetic field enhancements accompanied by thin current sheets at varying distances from the 19 sun and across different longitudes and latitudes. Two primary explanations have been proposed 20 to elucidate these phenomena: Solar wind-dust interaction and interlacing flux ropes. In this 21 study, we employ multi-fluid Magnetohydrodynamics (MHD) and Hall MHD models to simulate 22 these hypotheses, respectively. Our findings indicate a concurrence between both models and the 23 observed phenomena, suggesting that both processes may result in the same kind of 24 enhancement. Furthermore, both models make predictions pointing to additional types of 25 observational data, occurring at distinct spatial or temporal stages of the interaction. This 26 convergence of model predictions with empirical data underscores the need for further 27 observational and modeling studies to comprehensively test these models. This research 28 enhances our knowledge of the inner heliosphere's dynamics and the influence of the solar wind 29 on the Earth's magnetosphere, thereby shedding light on critical aspects of space weather and its 30 potential impact on our planet.
Supply of Subsidized Sale Flats and Private Housing Prices in Hong Kong

This paper investigates the association between the supply of subsidized sale flats by the Hong Kong Housing Authority and private residential property prices in Hong Kong, and their cause-and-effect relationships. The objective is to determine whether a sudden cessation of production and sale of the Home Ownership Scheme (HOS) and Private Sector Participation Scheme (PSPS) flats between September 2001 and end of June 2002, and indefinitely from 2003 onwards would encourage public tenants to buy in the private sector and subsequently increase private housing prices. The analysis is based on the supply of HOS/PSPS flats since its introduction in February 1978 until the last batch of flats sold in July 2002. The impact of supply restriction on private housing prices was examined. Using quarterly data for 1978-2003, the results show that housing prices move independently of the supply of these subsidized sale flats and that such supply does not “Granger cause” housing prices. The study has also found evidence that the cessation has not restored the market or resulted in any increase in housing prices. Finally, the private housing market is not affected by the implementation of the moratorium nor do the production and sale of subsidized sale flats pose a direct threat to the private housing sector in Hong Kong.
Draft Genome Sequence of Xylella fastidiosa Pear Leaf Scorch Strain in Taiwan

ABSTRACT The draft genome sequence of Xylella fastidiosa pear leaf scorch strain PLS229, isolated from the pear cultivar Hengshan (Pyrus pyrifolia) in Taiwan, is reported here. The bacterium has a genome size of 2,733,013 bp, with a G+C content of 53.1%. The PLS229 genome was annotated and has 3,259 open reading frames and 50 RNA genes.
Impacts of global environmental changes on water: challenges for sustainable development

Historically hydropower has been an important driver of economic and social development by providing both energy and water management services that generate multiplier effects (Kumar et al. 2009; van Vliet et al. 2012). By offering low-carbon energy and climate-adaptation benefits, hydropower will play an increasingly important role also in the future in the context of greenhouse gas mitigation. In the context of climate change adaptation, reservoirs could be used for irrigation and flood risk management. Yet, future climatic conditions are likely to affect the potential of this source of energy with uncertain consequences for its adaptive and mitigation capacity. Here we analyze the sensitivity of storage hydropower with reservoirs of different size and assess the magnitude and uncertainty of its vulnerability under future climate at global scale. Results indicate that changes in seasonal runoff patterns as well as variations in frequency and intensity of wet and dry conditions are expected to affect hydropower. Significant heterogeneity across unit size is found and the response varies with the ability of the hydropower facilities to cope with interand intra-annual variability by using their storage capacity. Globally, climate change impacts on hydropower resulting from our estimates appear equivocal and substantial variations existing even within countries. Yet, clear patterns can be identified for particular hydropower plants size in certain regions such as Southern Europe, North America, and Asia. 3 This Chapter is based on: Farinosi, F. , De Cian, E. , Sue Wing, I. (in preparation). “Vulnerability of Global Hydropower to Future Climate Change”
successful treatment of metastatic colorectal cancer with apatinib: report of two cases and literature review

: Apatinib, a novel small molecule tyrosine kinase inhibitor that inhibits vascular endothelial growth factor receptor-2, was approved for metastatic gastric adenocarcinoma in China in Oct 2014. This is the first report on its use for advanced colorectal cancer as a kind of third-line therapy to date. Here we report two Chinese patients who presented with metastatic colorectal cancer who received apatinib 850 mg daily as a third-line therapy. Both the patients achieved favorable benefits in outcomes after the administration of apatinib. Patient 1 benefited 4 months progression-free survival and 11 months overall survival, while patient 2’s progression-free survival was over 10 months. Both the patients presented hand–foot syndrome, and one of them suffered a slight impairment of liver function, mild elevated blood pressure, and proteinuria. But these adverse events were manageable with symptomatic treatment and dose reduction or a short-time drug withdrawal.
Evaluating the Economic Beneﬁts of Tightening Regulations on the Use of Toluene, a Hazardous Chemical, in South Korea

: The South Korean government currently designates toluene as a hazardous chemical, only limiting its use in products that are feared to be harmful. Since no measures to prohibit the use of toluene have been implemented, toluene is frequently detected in amounts that exceed the limit. Accordingly, the Government is considering implementing a plan to tighten the current regulations related to the use of toluene to prevent the occurrence of diseases caused by exposure and addiction to it. Therefore, the most important objective of this research is to evaluate quantitatively the economic beneﬁts arising from the implementation of the plan in South Korea. To achieve the purpose of this paper, contingent valuation, an economic technique for analyzing data collected from a survey of people based on economic theory, is applied. For this purpose, a survey of 1000 people nationwide is conducted, and an analysis model that is well received in the literature is adopted. In other words, the annual willingness to pay (WTP) per household to strengthen the regulations to reduce the human health risks of toluene is evaluated to calculate its economic beneﬁts. All the estimated WTP models secure statistical signiﬁcance. The average WTP per household per annum is derived as KRW 3394 (USD 3.02). Considering that the country contained 20,573,060 households in 2021, the national economic beneﬁts are calculated as KRW 69.82 billion (USD 62.23 million) every year. It is difﬁcult to estimate accurately the costs incurred by tightening the regulations on toluene use, but they do not seem to exceed the beneﬁts. Because tightening the regulations would be socially desirable, the Government would be justiﬁed in making this decision.