Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Basis of Rnd1 Binding to Plexin Rho GTPase Binding Domains (RBDs)*

Plexin receptors regulate cell adhesion, migration, and guidance. The Rho GTPase binding domain (RBD) of plexin-A1 and -B1 can bind GTPases, including Rnd1. By contrast, plexin-C1 and -D1 reportedly bind Rnd2 but associate with Rnd1 only weakly. The structural basis of this differential Rnd1 GTPase binding to plexin RBDs remains unclear. Here, we solved the structure of the plexin-A2 RBD in complex with Rnd1 and the structures of the plexin-C1 and plexin-D1 RBDs alone, also compared with the previously determined plexin-B1 RBD.Rnd1 complex structure. The plexin-A2 RBD·Rnd1 complex is a heterodimer, whereas plexin-B1 and -A2 RBDs homodimerize at high concentration in solution, consistent with a proposed model for plexin activation. Plexin-C1 and -D1 RBDs are monomeric, consistent with major residue changes in the homodimerization loop. In plexin-A2 and -B1, the RBD β3-β4 loop adjusts its conformation to allow Rnd1 binding, whereas minimal structural changes occur in Rnd1. The plexin-C1 and -D1 RBDs lack several key non-polar residues at the corresponding GTPase binding surface and do not significantly interact with Rnd1. Isothermal titration calorimetry measurements on plexin-C1 and -D1 mutants reveal that the introduction of non-polar residues in this loop generates affinity for Rnd1. Structure and sequence comparisons suggest a similar mode of Rnd1 binding to the RBDs, whereas mutagenesis suggests that the interface with the highly homologous Rnd2 GTPase is different in detail. Our results confirm, from a structural perspective, that Rnd1 does not play a role in the activation of plexin-C1 and -D1. Plexin functions appear to be regulated by subfamily-specific mechanisms, some of which involve different Rho family GTPases.
Thaumatin Production in Aspergillus awamori by Use of Expression Cassettes with Strong Fungal Promoters and High Gene Dosage

ABSTRACT Four expression cassettes containing strong fungal promoters, a signal sequence for protein translocation, a KEX protease cleavage site, and a synthetic gene (tha) encoding the sweet protein thaumatin II were used to overexpress this protein in Aspergillus awamori lpr66, a PepA protease-deficient strain. The best expression results were obtained with the gdhA promoter ofA. awamori or with the gpdA promoter ofAspergillus nidulans. There was good correlation oftha gene dosage, transcript levels, and thaumatin secretion. The thaumatin gene was expressed as a transcript of the expected size in each construction (1.9 or 1.4 kb), and the transcript levels and thaumatin production rate decayed at the end of the growth phase, except in the double transformant TB2b1-44-GD5, in which secretion of thaumatin continued until 96 h. The recombinant thaumatin secreted by a high-production transformant was purified to homogeneity, giving one major component and two minor components. In all cases, cleavage of the fused protein occurred at the KEX recognition sequence. This work provides new expression systems inA. awamori that result in very high levels of thaumatin production.
Characterization of the Core and Caste-Specific Microbiota in the Termite, Reticulitermes flavipes

The hindgut of the termite Reticulitermes flavipes harbors a complex symbiotic community consisting of protists, bacteria, and archaea. These symbionts aid in the digestion of lignocellulose from the termite’s wood meal. Termite hindguts were sampled and the V4 hyper-variable region of the 16S rRNA gene was sequenced and analyzed from individual termites. The core microbiota of worker termites consisted of 69 OTUs at the 97% identity level, grouped into 16 taxa, and together accounted for 67.05% of the sequences from the bacterial community. The core was dominated by Treponema, which contained 36 different OTUs and accounted for ∼32% of the sequences, which suggests Treponema sp. have an important impact on the overall physiology in the hindgut. Bray–Curtis beta diversity metrics showed that hindgut samples from termites of the same colony were more similar to each other than to samples from other colonies despite possessing a core that accounted for the majority of the sequences. The specific tasks and dietary differences of the termite castes could have an effect on the composition of the microbial community. The hindgut microbiota of termites from the alate castes differed from the worker caste with significantly lower abundances of Treponema and Endomicrobia, which dominated the hindgut microbiota in workers and soldiers. Protist abundances were also quantified in the same samples using qPCR of the 18S rRNA gene. Parabasalia abundances dropped significantly in the winged alates and the Oxymonadida abundances dropped in both alate castes. These data suggest that the changes in diet or overall host physiology affected the protist and bacterial populations in the hindgut. The in-depth bacterial characterization and protist quantification in this study sheds light on the potential community dynamics within the R. flavipes hindgut and identified a large and complex core microbiota in termites obtained from multiple colonies and castes.
Exponential Convergence of hp-Finite Element Discretization of Optimal Boundary Control Problems with Elliptic Partial Differential Equations

We investigate the numerical solution of boundary control problems with elliptic partial differential equations by the $hp$-finite element method. We prove exponential convergence with respect to the number of unknowns for an a priori chosen discretization. Here, we have to prove that derivatives of arbitrary order of the solution belong to suitably chosen weighted Sobolev spaces. This result relies on the assumption that the number of switching points of the optimal control is finite. Numerical experiments confirm the theoretical findings.
Abstraction-Based Heuristics with True Distance Computations

Pattern Databases (PDBs) are the most common form of memory-based heuristics, and they have been widely used in a variety of permutation puzzles and other domains. We explore the true-distance heuristics (TDHs) (also appeared in (Sturtevant et al. 2009)) which are a different form of memory-based heuristics, designed to work in problem states where there isn't a fixed goal state. Unlike PDBs, which build a heuristic based on distances in an abstract state space, TDHs store distances which are computed in the actual state space. We look in detail at how TDHs work, providing both theoretical and experimental motivation for their use.
Establishment of sink conditions in dissolution rate determinations. Theoretical considerations and application to nondisintegrating dosage forms.

The importance of approximating perfect sink conditions for the determination of dissolution rates which may be correlated with in vivo results is pointed out. A theoretical treatment of zero and first-order dissolution under perfect sink and nonsink conditions is presented. It is shown that unless sink conditions are maintained, in vitro results will bear little relationship to in vivo observations. The use of an organic solvent phase which can function as a reservoir for dissolved drug and thereby maintain sink conditions in the aqueous dissolution fluid is demonstrated for a model nondisintegrating tablet exhibiting zero-order drug release. The use of an organic solvent reservoir for the determination of first-order dissolution rates is also discussed.
A novel speed regulated algorithm for Surface Mounted Permanent Magnet Synchronous Motor

For the specifics of speed regulation of Surface Mounted Permanent Magnet Synchronous Motor (SPMSM), this paper presents a novel algorithm focused on phase-lead compensation and current estimation. Conventional speed control algorithm was commonly consisted of a speed regulator and a current regulator which based on Filed Orient Control (FOC), however, the complicated control scheme of FOC has brought several problems in industrial applications, such as phase current sampling. In order to simplifying the control scheme and enhancing the performance of the motor, a method of phase-lead compensation and current estimation is proposed. With this method, the FOC can be eliminated as well as current sample circuit and the motor can maintain nice performance of both dynamic and static just only with a single speed regulator. Finally, the effectiveness of the posed algorithm has been investigated through simulation results.
A vlHMM approach to context-aware search

Capturing the context of a user's query from the previous queries and clicks in the same session leads to a better understanding of the user's information need. A context-aware approach to document reranking, URL recommendation, and query suggestion may substantially improve users' search experience. In this article, we propose a general approach to context-aware search by learning a variable length hidden Markov model (vlHMM) from search sessions extracted from log data. While the mathematical model is powerful, the huge amounts of log data present great challenges. We develop several distributed learning techniques to learn a very large vlHMM under the map-reduce framework. Moreover, we construct feature vectors for each state of the vlHMM model to handle users' novel queries not covered by the training data. We test our approach on a raw dataset consisting of 1.9 billion queries, 2.9 billion clicks, and 1.2 billion search sessions before filtering, and evaluate the effectiveness of the vlHMM learned from the real data on three search applications: document reranking, query suggestion, and URL recommendation. The experiment results validate the effectiveness of vlHMM in the applications of document reranking, URL recommendation, and query suggestion.
Opportunities and Challenges in Generalizable Sensor-Based Affect Recognition for Learning

Recent years have witnessed major research advances in sensor- based affect recognition. Alongside these advances, there are many open ques- tions about how effectively current affective recognition techniques generalize to new populations and domains. We conducted a study of learner affect with a population of cadets from the U.S. Military Academy using a serious game about tactical combat casualty care. Using the study data, we sought to repro- duce prior affect recognition findings by inducing models that leveraged pos- ture-based predictor features that had previously been found to predict affect in other populations and learning environments. Our findings suggest that features and techniques, drawn from the literature but adapted to our setting, did not yield comparably effective models of affect recognition. Several of our affect recognition models performed only marginally better than chance, and one model actually performed worse than chance, despite using principled features and methods. We discuss the challenges of devising generalizable models of af- fect recognition using sensor data, as well as opportunities for improving the accuracy and generalizability of posture-based affect recognition.
Vector Gaussian Two-Terminal Source Coding

We derive a lower bound on each supporting line of the rate region of the vector Gaussian two-terminal CEO problem, which is a special case of the indirect vector Gaussian two-terminal source coding problem. The key technical ingredient is a new extremal inequality. It is shown that the lower bound coincides with the Berger-Tung upper bound in the high-resolution regime. Similar results are derived for the direct vector Gaussian two-terminal source coding problem.
Frequency-warping in speech

We present results that indicate that the formant frequencies between different speakers scale differently at different frequencies. Based on our experiments on speech data, we then numerically compute a universal frequency-warping function, to make the scale-factor independent of frequency in the warped domain. The proposed warping function is found to be similar to the mel-scale, which has previously been derived from purely psycho-acoustic experiments. The motivation for the present experiments stems from our proposed use of scale-transform based cepstral coefficients (Umesh et al., 1996) as acoustic features, since they provide superior separability of vowels than mel-cepstral coefficients.
Capture effect on downlink throughput of a CSMA based WLAN

We study the capture effect on the downlink throughput of a carrier sense multiple access (CSMA) based wireless local area network (WLAN) in presence of path loss, Rayleigh fading and log-normal shadowing. For this purpose, we develop an analytical model to compute the saturation throughput of the AP in a WLAN without and with the capture effect. The developed analytical model is then validated via simulation. By means of the analytical model, we determine the throughput increment due to the capture effect by computing the throughput of a WLAN without and with the capture effect. We find that the throughput increment due to the capture effect is very significant. We also investigate the effect of the variations of some network and wireless channel parameters on the increment of downlink throughput due to the capture effect. We find that the throughput increment due to the capture effect increases with increasing the user transmission probability and the variance of shadowing. However, the throughput increment due to the capture effect decreases with increasing the data transmission rate.
Generative Steganography with Kerckhoffs' Principle based on Generative Adversarial Networks

The distortion in steganography comes from the modification or recoding on the cover image during the embedding process. The changes of the cover always leave the steganalyzer with possibility of discriminating. Therefore, we propose to use a cover to send out secret messages without any modification by training the cover image to generate the secret messages. To ensure the security of such a generative scheme, we require the generator to meet Kerckhoffs' principle. Based on above proposal, we propose generative steganography with Kerckhoffs' principle (GSK) in this letter. In GSK, we use a generator based on generative adversarial networks (GAN) to output the secret messages if and only if the data-hiding key and the cover image are both inputted. Without the data-hiding key or the cover image, only meaningless results would be outputted. We detail the framework and the internal structure of GSK. In our training procedures, there are two GANs, Key-GAN and Cover-GAN, designed to work jointly making the generated results under the control of the data-hiding key and the cover image. Experimental results concentrate on the training process and the working performance of GSK which demonstrate that GSK can use any image to realize steganography with Kerckhoffs' principle without any modification.
Measurement of health‐related quality of life in multiple myeloma

When a randomized trial (NMSG 4/90) comparing treatment with melphalan/prednisone to melphalan/prednisone + interferon α‐2b in newly diagnosed multiple myeloma was inititated in 1990, a quality‐of‐life assessment was integrated into the study. We used the questionnaire (QLQ‐C30) developed by the European Organization of Research and Treatment of Cancer (EORTC) Study Group on Quality of Life. The QLQ‐C30 incorporates five functional scales, three symptom scales, a global health and quality‐of‐life scale and some single symptom measures. The questionnaire was completed prior to treatment and after 1, 6, 12, 24, 36 and 48 months. 524 (90.2%) of 581 patients enrolled in the NMSG 4/90 completed the first questionnaire, and 484 (83.3%) completed all questionnaires given to them. All but one of the scales met the minimum criteria of reliability (Cronbach’s alpha ≥0.70). Validity was shown by (1) the ability of the scales to discriminate clearly between patients differing in clinical status as defined by pre‐treatment W.H. O. performance index and Durie & Salmon stage, and (2) the sensitivity to changes in objective disease status (response and relapse). This is the first report of the measurement of health‐related quality of life in a prospective clinical trial in multiple myeloma. The results demonstrate that the QLQ‐C30 is a reliable and valid instrument for the measurement of quality of life in these patients. The data will be used for a cost–utility analysis of the results of the NMSG 4/90 trial.
A Generalized Finite Element Method for polycrystals with discontinuous grain boundaries

We present a Generalized Finite Element Method for the analysis of polycrystals with explicit treatment of grain boundaries. Grain boundaries and junctions, understood as loci of possible displacement discontinuity, are inserted into finite elements by exploiting the partition of unity property of finite element shape functions. Consequently, the finite element mesh does not need to conform to the polycrystal topology. The formulation is outlined and a numerical example is presented to demonstrate the potential and accuracy of the approach. The proposed methodology can also be used for branched and intersecting cohesive cracks, and comparisons are made to a related approach (Int. J. Numer. Meth. Engng. 2000; 48:1741). Copyright © 2006 John Wiley & Sons, Ltd.
Interferon- (cid:1) , a Th1 Cytokine, Regulates Fat Inflammation A Role for Adaptive Immunity in Obesity

—Adipose tissue (AT) can accumulate macrophages and secrete several inflammatory mediators. Despite its pivotal role in the progression of chronic inflammatory processes such as atherosclerosis, the adaptive role of immunity in obesity remains poorly explored. Visceral AT of diet-induced obese C57BL/6 mice had higher numbers of both CD4 (cid:1) and CD8 (cid:1) T cells than lean controls, monitored by flow cytometry. When stimulated in vitro, T cells from obese AT produced more interferon (IFN) (cid:1) than those from controls. AT from obese animals also had more cells expressing I-A b , a mouse class II histocompatibility marker implicated in antigen presentation, as determined by immunostaining. Differentiated 3T3-L1 cells stimulated with recombinant IFN (cid:1) or T-helper 1–derived supernatant produced several chemokines and their mRNAs. Obese IFN (cid:1) -deficient animals had significantly reduced AT expression of mRNA-encoding inflammatory genes such as tumor necrosis factor- (cid:2) and monocyte chemoattractant protein-1, decreased AT inflammatory cell accumulation, and better glucose tolerance than control animals consuming the same diet. Obese mice doubly deficient for IFN (cid:1) receptor and apolipoprotein (Apo)E on a mixed 129SvEv/C57BL/6 (129/B6) genetic background, despite exhibiting similar AT mRNA levels of tumor necrosis factor- (cid:2) and monocyte chemoattractant protein-1 as 129/B6-ApoE (cid:2) / (cid:2) controls, had decreased expression of important T cell–related genes, such as IFN (cid:1) -inducible protein-10 and I-A b , and lower plasma triglycerides and glucose. These results indicate a role for T cells and IFN (cid:1) , a prototypical T-helper 1 cytokine, in regulation of the inflammatory response that accompanies obesity. ( Circ role cells in study a greater number of T cells in the of in the present study examined the participation of T cells, particularly of the signature Th1 cytokine IFN (cid:1) , in the setting of fat inflammation. In vitro data show that IFN (cid:1) modulates PCR was performed in a MyiQ Single-Color Real-Time PCR Detection System (Bio-Rad). The sequences of mouse primers used are described in the online data supplement. The mRNA levels of the various genes tested were normalized to glyceraldehyde 3-phosphate dehydrogenase (GAPDH), used as an internal control in all experiments.
Combined Analog and Digital Error-Correcting Codes for Analog Information Sources

This paper focuses on error-correcting codes for analog signals. Generally, error-correcting codes exhibit a threshold effect, which degrades performance at the low signal-to-noise ratio (SNR) range. We propose two error-correction alternatives based on chaotic dynamical systems, which improve threshold performance relative to previously proposed methods. The first one, which is based on principles of diversity, exhibits a very simple decoder. The second alternative, which is based on a low-density parity-check (LDPC) code, attains a significantly lower threshold. Theoretical analysis and simulations are provided.
Characterization of two new zebrafish members of the hedgehog family: Atypical expression of a zebrafish indian hedgehog gene in skeletal elements of both endochondral and dermal origins

We have characterized two new members of the Hedgehog (Hh) family in zebrafish, ihha and dhh, encoding for orthologues of the tetrapod Indian Hedgehog (Ihh) and Desert Hedgehog (Dhh) genes, respectively. Comparison of ihha and Type X collagen (col10a1) expression during skeletal development show that ihha transcripts are located in hypertrophic chondrocytes of cartilaginous elements of the craniofacial and fin endoskeleton. Surprisingly, col10a1 expression was also detected in cells forming intramembranous bones of the head and in flat cells surrounding cartilaginous structures. The expression of col10a1 in both endochondral and intramembranous bones reflects an atypical composition of the extracellular matrix of the zebrafish craniofacial skeleton. In addition, during fin ray regeneration, both ihha and col10a1 are detected in scleroblasts, osteoblast‐like cells secreting the matrix of the dermal bone fin ray. The presence of cartilage markers suggests that the dermal fin ray possesses an intermediate phenotype between cartilage and bone. Developmental Dynamics 235:478–489, 2006. © 2005 Wiley‐Liss, Inc.
High Mitochondrial DNA T8993G Mutation (>90%) Without Typical Features of Leigh's and NARP Syndromes

Neuropathy, ataxia, and retinitis pigmentosa (NARP) syndrome and maternally inherited Leigh's syndrome have been associated with T8993G point mutations in the mitochondrial adenosine triphosphatase 6 gene. Typically, NARP syndrome is characterized by developmental delay, seizures, dementia, retinitis pigmentosa, ataxia, sensory neuropathy, and proximal weakness. Usually, there is a correlation between the percentage of mutated mitochondrial DNA and clinical severity, and when mutated mitochondrial DNA is > 90%, it is often seen with Leigh's syndrome. We now report a family with mitochondrial DNA T8993G mutation in eight living members, five with mutant mitochondrial DNA >90% and one with 20% mutant mitochondrial DNA. However, their clinical features include variable combinations of seizures, behavior problems, learning disability, mental retardation, sensorineural deafness, cerebellar ataxia, and proximal muscle weakness. No retinitis pigmentosa was found in all eight living members, including a 56-year-old grandmother. Only one dead female relative was diagnosed with Leigh's syndrome on the neuropathologic examination at age 22 years, when she died of an accident. High mitochondrial DNA T8993G mutation is not always associated with typical features of Leigh's and NARP syndromes. (J Child Neurol 2001;16:533-535).