Miracle-dz/UniFAR-FTUs huggingface dataset:
Proline residues of transmembrane domains determine the sorting of inner membrane proteins in mitochondria

Most inner membrane proteins of mitochondria are synthesized in the cytosol and reach the inner membrane using one of two alternative sorting pathways. On the stop transfer route, proteins are arrested during import at the level of the inner membrane. The conservative sorting pathway involves translocation through the inner membrane and insertion from the matrix. It is unclear how the translocase of the inner membrane 23 protein translocation machinery differentiates between the two classes of proteins. Here we show that proline residues in hydrophobic stretches strongly disfavor the translocation arrest of transmembrane domains (TMDs) and favor the transfer of preproteins to the matrix. We propose that proline residues, together with the hydrophobicity of the TMD and the presence of charged residues COOH-terminally flanking the TMD, are determinants of the intramitochondrial sorting of inner membrane proteins.
Piezoelectric ultrasonic micromotors

This report describes development of micro-fabricated piezoelectric ultrasonic motors and bulk-ceramic piezoelectric ultrasonic motors. Ultrasonic motors offer the advantage of low speed, high torque operation without the need for gears. They can be made compact and lightweight and provide a holding torque in the absence of applied power, due to the traveling wave frictional coupling mechanism between the rotor and the stator. This report covers modeling, simulation, fabrication and testing of ultrasonic motors. Design of experiments methods were also utilized to find optimal motor parameters. A suite of 8 mm diameter x 3 mm tall motors were machined for these studies and maximum stall torques as large as 10^(- 3) Nm, maximum no-load speeds of 1710 rpm and peak power outputs of 27 mW were realized. Aditionally, this report describes the implementation of a microfabricated ultrasonic motor using thin-film lead zirconate titanate. In a joint project with the Pennsylvania State University Materials Research Laboratory and MIT Lincoln Laboratory, 2 mm and 5 mm diameter stator structures were fabricated on 1 micron thick silicon nitride membranes. Small glass lenses placed down on top spun at 100-300 rpm with 4 V excitation at 90 kHz. The large power densities and stall torques of these piezoelectric ultrasonic motors offer tremendous promis for integrated machines: complete intelligent, electro-mechanical autonomous systems mass-produced in a single fabrication process.
Teaching Through Toponymy: Using Indigenous Place-Names in Outdoor Science Camps

The naming o f places, be they landforms, villages or cities, is a cultural phenomenon dating back to the earliest o f times. Naming to identify and differentiate places seems to be as basic a need as assigning names to the persons and objects that make up one’s world. In the T l’azt’en culture, where oral transmission was the means o f passing down knowledge, people developed particular strategies for recalling information. Routes to hunting grounds or fishing holes, for instance, were memorized with the aid of place-names and through the narratives that illumined the named places. This study examines the potential o f Dakelh place-names as a tool for educating Tl’azt’en children and youth about the Tl’azt’en ancestral past, the Dakelh language and places on the land that have sustained Tl’azt’enne for generations. The processes o f colonization, resistance and cultural reclamation as observed in the naming and re-naming o f places provides a theoretical framework from which to explore the potential o f indigenous place-names to address issues of cultural revitalization and identity-strengthening. Such theory enables understanding of the importance o f indigenous language and places on the land in sustaining cultural identity and forming the basis for appreciating oral tradition. Nine o f the eleven toponyms selected by Tl’azt’en Nation were used in this thesis research for analysis; interviews with TPazt’en cultural experts and secondary source material were used to assemble and verify the place-names information (their accuracy in terms o f location, spelling and meaning), their geographical referents as well as the topographic, biotic and cultural use descriptions for the places they mark. This thesis shows that there is a considerable wealth o f Traditional Ecological Knowledge contained in Dakelh place-names, namely knowledge linked to travel and subsistence, and information pertaining to spirituality and the ancestral past. Five guidelines for teaching
Partition function game for rate optimization in random interference networks

Interference is one of the main limiting factors in wireless communication networks for system performance nowadays. In this paper, we study a coalitional game approach for rate optimization in a random interference networks where multiple transmission pairs transmit concurrently. We model the rate optimization problem as a partition function game. All transmission pairs form separated coalitions, and the pairs cooperate to transmit within each coalition. An iterative coalition structure generation algorithm is proposed to obtain partitions. This algorithm allows each transmission pair to make individual decision whether to stay in or depart from its current coalition. We prove that the proposed iterative algorithm can achieve a Nash-stable partition. In each coalition, we adopt the duality features of broadcast channel (BC) and multi-access channel (MAC) to maximize the sum-rate. Simulation results show that the proposed algorithm can improve the network performance significantly compared with location-based static partition forms.
Synaptotagmin Regulation of Coated Pit Assembly*

Synaptotagmins bind clathrin AP-2 with high affinity via their second C2 domain, which indicates they are involved in coated pit function. We now report that expression of synaptotagmins lacking either the second C2 domain or the entire cytoplasmic region potently inhibit endocytosis. Inhibition was dependent on two intramembrane cysteine residues that were found to be essential for synaptotagmin oligomerization. Cells expressing the wild-type, but not the mutant, truncated synaptotagmin fragment had a reduced number of clathrin-coated pits. These results suggest that the formation of synaptotagmin multimers is an important step in the regulation of coated pit assembly.
Maresin Biosynthesis and Identification of Maresin 2, a New Anti-Inflammatory and Pro-Resolving Mediator from Human Macrophages

Maresins are a new family of anti-inflammatory and pro-resolving lipid mediators biosynthesized from docosahexaenoic acid (DHA) by macrophages. Here we identified a novel pro-resolving product, 13R,14S-dihydroxy-docosahexaenoic acid (13R,14S-diHDHA), produced by human macrophages. PCR mapping of 12-lipoxygenase (12-LOX) mRNA sequence in human macrophages and platelet showed that they are identical. This human 12-LOX mRNA and enzyme are expressed in monocyte-derived cell lineage, and enzyme expression levels increase with maturation to macrophages or dendritic cells. Recombinant human 12-LOX gave essentially equivalent catalytic efficiency (kcat/KM) with arachidonic acid (AA) and DHA as substrates. Lipid mediator metabololipidomics demonstrated that human macrophages produce a novel bioactive product 13,14-dihydroxy-docosahexaenoic acid in addition to maresin-1, 7R,14S-dihydroxy-4Z,8E,10E,12Z,16Z,19Z-docosahexaenoic acid (MaR1). Co-incubations with human recombinant 12-LOX and soluble epoxide hydrolase (sEH) demonstrated that biosynthesis of 13,14-dihydroxy-docosahexaenoic acid (13,14-diHDHA) involves the 13S,14S-epoxy-maresin intermediate produced from DHA by 12-LOX, followed by conversion via soluble epoxide hydrolase (sEH). This new 13,14-diHDHA displayed potent anti-inflammatory and pro-resolving actions, and at 1 ng reduced neutrophil infiltration in mouse peritonitis by ∼40% and at 10 pM enhanced human macrophage phagocytosis of zymosan by ∼90%. However, MaR1 proved more potent than the 13R,14S-diHDHA at enhancing efferocytosis with human macrophages. Taken together, the present findings demonstrate that macrophages produced a novel bioactive product identified in the maresin metabolome as 13R,14S-dihydroxy-docosahexaenoic acid, from DHA via conversion by human 12-LOX followed by sEH. Given its potent bioactions, we coined 13R,14S-diHDHA maresin 2 (MaR2).
Improving the Forward Link of the Future AirportData Link by Space-Time Coding

In the context of the future communication system for the airport surface operations (AeroMACS), we investigate the 2×1 Alamouti scheme applied to the 802.16e standard for improving the performance of the forward link. We propose a novel space-time coding realization which preserves the original frame structure of WiMAX, analyzing its performance in a realistic airport environment. Simulation results show the performance of the system over different scenarios.
Bridging the Gap between Systems Design and Space Systems Software

A challenging problem for software engineering practitioners is moving from high-level system architectures produced by system engineers to deployable software produced by software engineers. In this paper we describe our experience working with NASA engineers to develop an approach and toolset for automating the generation of space systems software from architectural specifications. Our experience shows that it is possible to leverage the space systems domain, formal architectural specifications, and component technology to provide retargetable code generators for this class of software.
I’ve lost the person I used to be—Experiences of the consequences of fatigue following myocardial infarction

Fatigue has been found to be the most frequent and bothersome symptom after myocardial infarction (MI), influencing health-related quality of life negatively. Moreover, fatigue after MI has been described as incomprehensible due to its unpredictable occurrence and lack of relationship to physical effort. The aim of this study is therefore to explore persons’ experiences of consequences of fatigue and their strategies for dealing with it 2 months after MI. In total, 18 informants, aged 42–75 years, participated in the study. Interviews were conducted and analysed using constructivist grounded theory methodology. Grounded in the data, the main consequence of fatigue, as illustrated in the core category, was: I've lost the person I used to be. It indicates a sense of reduced ability to manage daily life due to experiences of fatigue. The core category was developed from the four categories: involuntary thoughts, certainties replaced with question marks, driving with the handbrake on and just being is enough. Furthermore, attempts to relieve fatigue were limited. These findings indicate that patients with symptoms of fatigue should be supported in developing relief strategies, for example, rest and sleep hygiene as well as physical activity. In conclusion, the results show that fatigue can be understood in light of the concepts “comprehensibility” and “manageability. ” They also indicate that, working from a person-centered perspective, health-care professionals can support patients experiencing post-MI fatigue by giving them opportunities to straighten out the question marks and by inviting them to discuss involuntary thoughts and feelings of being restricted in their daily life functioning.
Designing a Virtual Manikin Animation Framework Aimed at Virtual Prototyping

In the industry, numerous commercial packages provide tools to introduce, and analyse human behaviour in the product's environment (for maintenance, ergonomics.), thanks to Virtual Humans. We will focus on control. Thanks to algorithms newly introduced in recent research papers, we think we can provide an implementation, which even widens, and simplifies the animation capacities of virtual manikins. In order to do so, we are going to express the industrial expectations as for Virtual Humans, without considering feasibility (not to bias the issue). The second part will show that no commercial application provides the tools that perfectly meet the needs. Thus we propose a new animation framework that better answers the problem. Our contribution is the integration - driven by need ~ of available new scientific techniques to animate Virtual Humans, in a new control scheme that better answers industrial expectations.
Actin filaments elongate from their membrane-associated ends

In limulus sperm an actin filament bundle 55 mum in length extends from the acrosomal vacuole membrane through a canal in the nucleus and then coils in a regular fashion around the base of the nucleus. The bundle expands systematically from 15 filaments near the acrosomal vacuole to 85 filaments at the basal end. Thin sections of sperm fixed during stages in spermatid maturation reveal that the filament bundle begins to assemble on dense material attached to the acrosomal vacuole membrane. In micrographs fo these early stages in maturation, short bundles are seen extending posteriorly from the dense material. The significance is that these short, developing bundles have about 85 filaments, suggesting that the 85-filament end of the bundle is assembled first. By using filament bundles isolated and incubated in vitro with G actin from muscle, we can determine the end “preferred” for addition of actin monomers during polymerization. The end that would be associated with the acrosomal vacuole membrane, a membrane destined to be continuous with the plasma membrane, is preferred about 10 times over the other, thicker end. Decoration of the newly polymerized portions of the filament bundle with subfragment 1 of myosin reveals that the arrowheads point away from the acrosomal vacuole membrane, as is true of other actin filament bundles attached to membranes. From these observations we conclude that the bundle is nucleated from the dense material associated with the acrosomal vacuole and that monomers are added to the membrane-associated end. As monomers are added at the dense material, the thick first-made end of the filament bundle is pushed down through the nucleus where, upon reaching the base of the nucleus, it coils up. Tapering is brought about by the capping of the peripheral filaments in the bundle.
A statistical method of analyzing global gene expression data obtained from experiments using Japanese herbal medicine

Japanese herbal medicines (Kampo) are characterized by the diseases and the combination of multiple galenicals to enhance their action through synergistic effects and to minimize adverse effects [1]. It is necessary for systems biology of oriental traditional medicines to determine genes influenced by those medicines. However, there is bias in gene expression data concerning patients and source and quality of galenicals and other unknown causes. Their combined effects make it difficult to detect significantly expressed genes. In the present study, we propose a method using clustering of datasets and check its usefulness to analyze gene expression data of experiments using Toki-Shakuyaku-san.
PARMA: A Predicate Argument Aligner

We introduce PARMA, a system for crossdocument, semantic predicate and argument alignment. Our system combines a number of linguistic resources familiar to researchers in areas such as recognizing textual entailment and question answering, integrating them into a simple discriminative model. PARMA achieves state of the art results on an existing and a new dataset. We suggest that previous efforts have focussed on data that is biased and too easy, and we provide a more difficult dataset based on translation data with a low baseline which we beat by 17% F1.
Hydrogen-bond interactions in morpholinium bromide

In the title compound, C4H10NO+·Br−, which was synthesized by dehydration of diethanolamine with HBr, morpholinium and bromide ions are linked into chains by N—H⋯Br hydrogen bonds describing a C 2 1(4) graph-set motif. Weaker bifurcated N—H⋯Br interactions join centrosymmetrically related chains through alternating binary graph-set R 4 2(8) and R 2 2(4) motifs, to form ladders along [100]. In addition, C—H⋯O interactions between centrosymmetric morpholinium cations link ladders, via (8) motifs, to yield sheets parallel to (101), which in turn are crosslinked by weak C—H⋯O interactions, related across a glide plane, to form a three-dimensional network.
Using prosody for automatically monitoring human-computer call dialogues

In human-computer call dialogues, human callers often get frustrated or angry due to, e.g., the computer’s mistakes. Detecting such emotions would be beneficial for many purposes; nevertheless, emotion detection so far has been studied primarily as a classification task. Taking a step forward from classifying emotions from a single utterance, this paper investigates whether emotions, detected by prosodic features, can be used practically at the dialogue level, i.e., for monitoring human-computer dialogues to detect BAD calls requiring human agent’s assistance. We first show emotion detection can be improved by a regression model. In combining emotion detection and dialogue monitoring, we demonstrate decision level fusion is better than feature level fusion. Our experiments also confirm that NEGATIVE emotions may be a sufficient, but not a necessary condition for detecting BAD calls. Finally, we show that BAD calls due to caller’s NEGATIVE emotions may be identified by other clues.
Effects of agriculture, climate, and policy on NDVI change in a semi-arid river basin of the Chinese Loess Plateau

Abstract In 1999, the Grain for Green Project was implemented by the Chinese government. Since then, the vegetation of Zuli River Basin, a semi-arid river basin of the Chinese Loess Plateau, has been greatly changed. Clearly understanding the impact of natural and artificial factors on vegetation change is important for policy making and ecosystem management. In this study, spatio-temporal variations in vegetation cover in Chinese Zuli River Basin during 1999–2016 were investigated using Landsat normalized difference vegetation index (NDVI) data. Analyses of several indicators, including changes in NDVI in different slopes and land use changes and the relationships between climatic factors and NDVI change, were presented to quantitatively evaluate the effects of agriculture, climate, and policy on NDVI change. The NDVI in the Zuli River Basin increased during the study period, and the main contributors to this change were forest in 1999–2011, cropland, abandoned farmland, and grassland in 2009–2016, and land with slopes ≤ 15°. Land with slope > 15°, where the “Project” was implemented, slightly contributed to the increase in regional NDVI. In 1999–2011, the project (−98.16%) combined with climate change (−68.18%) showed negative effects on the increase in NDVI in the Zuli River Basin, but agriculture (22.28%) played a positive role in increasing this index. In 2009–2016 and 1999–2016, the project (38.45% and 35.25%, respectively), the project combined with climate change (49.83% and 46.30%, respectively), agriculture (18.61% and 23.30%, respectively), promoted increases in NDVI in the basin.
Automatic detection of bicycle direction using RealAdaBoost and C4.5

In recent years, there has been a decrease in the number of traffic accidents and deaths due to the improved vehicle safety and legislation related to traffic violations. However, the number of injuries is still large, with injuries incurred by bicyclists and pedestrians accounting for approximately 25% of the total number of injuries. Measures must be taken to ensure the safety of pedestrians and bicyclists, which is an important issue. This study, which proposes a system for automatically detecting the direction in which a bicycle is moving, is a contribution to the development of an overall support system for safe automobile driving.
Eurographics/ Acm Siggraph Symposium on Computer Animation (2008) Synthesis of Interactive Hand Manipulation

We present an interactive physics-based motion synthesis technique for creating hand manipulation across a wide variety of tasks, objects, user interventions, and stylistic preferences. Given an object being manipulated, a single pose specifying the desired initial contact, and the kinematic goals of the manipulation, our algorithm automatically generates hand-object manipulation that is responsive to unscripted external disturbances. Our algorithm simulates the dynamic coupling between a passive dynamic system and an active dynamic system by formulating a sequence of constrained optimizations. This formulation allows the user to synthesize a manipulation task by describing simple, keyframe-like kinematic goals in the domain of object configuration. The algorithm will automatically produce the hand motion that achieves the kinematic goals via coupled dynamic equations of motion.
Long-term exercise attenuates blood pressure responsiveness and modulates kidney angiotensin II signalling and urinary sodium excretion in SHR

Observations have been made regarding the effects of long-term exercise training on blood pressure, renal sodium handling and renal renin–angiotensin–aldosterone (RAS) intracellular pathways in conscious, trained Okamoto–Aoki spontaneously hypertensive rats (SHR) and Wistar Kyoto (WKy) normotensive rats, compared with appropriate age-matched sedentary SHR and WKy. To evaluate the influence of exercise training on renal function and RAS, receptors and intracellular angiotensin II (AngII) pathway compounds were used respectively, and lithium clearance and western blot methods were utilised. The current study demonstrated that increased blood pressure in SHR was blunted and significantly reduced by long-term swim training between the ages of 6 and 16 weeks. Additionally, the investigators observed an increased fractional urinary sodium excretion in trained SHR (SHRT) rats, compared with sedentary SHR (SHRS), despite a significantly decreased creatinine clearance (CCr). Furthermore, immunoblotting analysis demonstrated a decreased expression of AT1R in the entire kidney of TSHR rats, compared with SSHR. Conversely, the expression of the AT2R, in both sedentary and trained SHR, was unchanged. The present study may indicate that, in the kidney, long-term exercise exerts a modulating effect on AngII receptor expression. In fact, the present study indicates an association of increasing natriuresis, reciprocal changes in renal AngII receptors and intracellular pathway proteins with the fall in blood pressure levels observed in TSHR rats compared with age-matched SSHR rats.
In praise of the referee

There has been a lively debate in many fields, including statistics and related applied fields such as psychology and biomedical research, on possible reforms of the scholarly publishing system. Currently, referees contribute so much to improve scientific papers, both directly through constructive criticism and indirectly through the threat of rejection. We discuss ways in which new approaches to journal publication could continue to make use of the valuable efforts of peer reviewers.
Real-Time Procurement Strategies of a Proactive Distribution Company With Aggregator-Based Demand Response

In this paper, we present a real-time trading framework for distribution networks where a rational aggregator is identified as a broker by contracting with individual demands and dealing with the distribution company. Demand response capability is characterized by the coexistence of elastic and inelastic demand components. A one-leader multi-follower bi-level model is proposed to derive the procurement strategies, i.e., the upper-level problem intends to maximize the profit of the proactive distribution company, while the lower-level expresses the profit maximization per rational aggregator. The proposed model is then transformed into a solvable mathematical program with equilibrium constraints through a primal-dual approach. A modified 33-bus distribution network is utilized to demonstrate the effectiveness of the proposed model.