Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteins with amino acid repeats constitute rapidly evolvable and human-specific essentialome

Protein products of essential genes, indispensable for organismal survival, are highly conserved and bring about fundamental functions. Interestingly, proteins that contain amino acid homorepeats that tend to evolve rapidly are enriched in eukaryotic essentialomes. Why are proteins with hypermutable homorepeats enriched in conserved and functionally vital essential proteins? We solve this function versus evolutionary paradox by demonstrating that human essential proteins with homorepeats bring about cross-talk across biological processes through high interactability and have distinct regulatory functions affecting expansive global regulation. Importantly, essential proteins with homorepeats rapidly diverge with the amino acid substitutions frequently affecting functional sites, likely facilitating rapid adaptability. Strikingly, essential proteins with homorepeats influence human-specific embryonic and brain development, implying that the presence of homorepeats could contribute to the emergence of human-specific processes. Thus, we propose that homorepeat containing essential proteins affecting species-specific traits can be potential intervention targets across pathologies including cancers and neurological disorders.
The BRUTUS-LIKE E3 ligases BTSL1 and BTSL2 fine-tune transcriptional responses to balance Fe and Zn homeostasis

The mineral micronutrients zinc (Zn) and iron (Fe) are essential for plant growth and human nutrition, but interactions between the homeostatic networks of these two elements are not fully understood. Here we show that loss-of-function of BTSL1 and BTSL2, which encode partially redundant E3 ubiquitin ligases that negatively regulate Fe uptake, confers tolerance to Zn excess in Arabidopsis thaliana. Double btsl1 btsl2 mutant seedlings grown on high Zn medium accumulated similar amounts of Zn in roots and shoots as the wild type, but suppressed the accumulation of excess Fe in roots. RNA-seq analysis showed that roots of mutant seedlings had relatively higher expression of genes involved in Fe uptake (IRT1, FRO2, NAS) and in Zn storage (MTP3, ZIF1). Surprisingly, mutant shoots did not show the transcriptional Fe-deficiency response which is normally induced by Zn excess. Split-root experiments suggested that within roots the BTSL proteins act locally and downstream of systemic Fe deficiency signals. Together, our data show that constitutive low-level induction of the Fe-deficiency response protects btsl1 btsl2 mutants from Zn toxicity. We propose that BTSL protein function is disadvantageous in situations of external Zn and Fe imbalances, and formulate a general model for Zn-Fe interactions in plants. Highlight Mutation of two E3 ligases that suppress iron uptake in roots also confers tolerance to zinc toxicity, identifying a regulatory point of interaction between iron and zinc homeostasis.
Starvation sensing by mycobacterial RelA/SpoT homologue through constitutive surveillance of translation

The stringent response, which leads to persistence of nutrient-starved mycobacteria, is induced by activation of the RelA/SpoT homologue (Rsh) upon entry of a deacylated-tRNA in a translating ribosome. However, the mechanism by which Rsh identifies such ribosomes in vivo remains unclear. Here, we show that conditions inducing ribosome hibernation result in loss of intracellular Rsh in a Clp protease-dependent manner. This loss is also observed in non-starved cells using mutations in Rsh that block its interaction with the ribosome, indicating that Rsh association with the ribosome is important for Rsh stability. The cryo-EM structure of the Rsh-bound 70S ribosome in a translation initiation complex reveals unknown interactions between the ACT domain of Rsh and components of the ribosomal L7/L12-stalk base, suggesting that the aminoacylation status of A-site tRNA is surveyed during the first cycle of elongation. Altogether, we propose a surveillance model of Rsh activation that originates from its constitutive interaction with the ribosomes entering the translation cycle. Significance Bacteria persist under nutrient starvation by activating RelA/SpoT homologue (Rsh), which synthesizes a growth regulating alarmone, ppGpp. Rsh is activated specifically upon recognizing a translation elongation complex with deacylated tRNA at the A-site. It is however unclear how Rsh identifies such a complex in vivo. We show here that conditions inducing ribosome hibernation in mycobacteria cause loss of intracellular Rsh, implying that association with translating ribosomes is necessary for intracellular stability of Rsh. Using structural analysis of Rsh-bound 70S translation initiation complex, we propose here that mycobacterial Rsh identifies a Rsh-activating ribosomal complex by constitutively surveying the ribosome entering the translation cycle at the early elongation stage.
The Development of Object Recognition Requires Experience with the Surface Features of Objects

What role does visual experience play in the development of object recognition? Prior controlled-rearing studies suggest that newborn animals require slow and smooth visual experiences to develop object recognition. Here we examined whether the development of object recognition also requires experience with the surface features of objects. We raised newborn chicks in automated controlled-rearing chambers that contained a single virtual object, then tested their ability to recognize that object from familiar and novel viewpoints. When chicks were reared with an object that had surface features, the chicks developed view-invariant object recognition. In contrast, when chicks were reared with a line drawing of an object, the chicks failed to develop object recognition. The chicks reared with line drawings performed at chance level, despite acquiring over 100 hours of visual experience with the object. These results indicate that the development of object recognition requires experience with the surface features of objects.
MicroRNA-205 promotes hair regeneration by modulating mechanical properties of hair follicle stem cells

Stiffness and actomyosin contractility are intrinsic mechanical properties of animal cells required for the shaping of tissues. However, whether tissue stem cells (SCs) and progenitors located within SC niche have different mechanical properties that govern their size and functions remains unclear. We show that hair follicle SCs in the bulge are stiff with high actomyosin contractility and resistant to size change, whereas hair germ (HG) progenitors are soft and periodically enlarge and contract during quiescence. During activation, HGs reduce contraction and more frequently enlarge, a process that is associated with weakening of the actomyosin network, nuclear YAP accumulation and cell cycle re-entry. Induction of miR-205, a novel regulator of the actomyosin cytoskeleton, reduces actin contractility, decreases the stiffness of the bulge and HG, and activates hair regeneration in young and old mice. This study reveals the control of tissue SC size and activities by spatiotemporally compartmentalized mechanical properties and demonstrates the possibility to stimulate tissue regeneration by fine-tuning cell mechanics.
Functionally analogous body- and animacy-responsive areas in the dog (Canis familiaris) and human occipito-temporal lobe

Comparing the neural correlates of socio-cognitive skills across species provides insights into the evolution of the social brain and has revealed face- and body-sensitive regions in the primate temporal lobe. Although from a different lineage, dogs share convergent visuo-cognitive skills with humans and a temporal lobe which evolved independently in carnivores. We investigated the neural correlates of face and body perception in dogs (N = 15) and humans (N = 40) using functional MRI. Combining univariate and multivariate analysis approaches, we found functionally analogous occipito-temporal regions involved in the perception of animate entities and bodies in both species, while only humans had regions specialized for face perception. Though unpredicted, we also observed neural representations of faces compared to inanimate objects, and dog compared to human bodies in dog olfactory regions. These findings shed light on the evolutionary foundations of human and dog social cognition and the predominant role of the temporal lobe.
Asymptotic Stabilization of Two-Wheeled Mobile Robot via Locally Semiconcave Generalized Homogeneous Control Lyapunov Function

: A locally semiconcave control Lyapunov function exists for every globally asymptotically controllable system; however for nonholonomic systems, the issue of a locally semiconcave generalized homogeneous control Lyapunov function is not investigated. In this paper, the authors propose a locally semiconcave generalized homogeneous control Lyapunov function for Brockett integrator as a canonical form of nonholonomic systems. Moreover, the authors propose an exponentially stabilizing controller for a two-wheeled mobile robot with the function. The e ﬀ ectiveness of the proposed method are conﬁrmed by computer simulation and an experiment, and advantages over previously proposed controllers are conﬁrmed by experiments.
Functionally dissecting claustrum along anterior-posterior axis in anxiety and higher sensitivity to cocaine

Adolescent cocaine exposure (ACE) induce anxiety and higher sensitivity to drug addiction during adulthood. Here, we show that the claustrum is crucial for control of these two distinct psychiatric disorders in ACE mice. In the process of anxiety test, the CaMKII-positive neurons in median portion of claustrum (MClaustrum) were obviously triggered, and chemogenetic suppressing these neurons efficiently reduced ACE-induced anxiety in adulthood. While, the CaMKII-positive neurons in anterior portion of claustrum (AClaustrum) were obviously activated in response to cocaine-induced conditioned place preference (CPP), and chemogenetic suppressing these neurons efficiently blocked cocaine CPP in ACE mice during adulthood. Our findings dissociating specific sub-portions of claustrum for drug-related anxiety and susceptibility of addiction, extending our understanding to diverse functions of claustrum subregions.
A stochastic world model on gravity for stability inference

The fact that objects without proper support will fall to the ground is not only a natural phenomenon, but also common sense in mind. Previous studies suggest that humans may infer objects’ stability through a world model that performs mental simulations with a priori knowledge of gravity acting upon the objects. Here we measured participants’ sensitivity to gravity to investigate how the world model works. We found that the world model on gravity was not a faithful replica of the physical laws, but instead encoded gravity’s vertical direction as a Gaussian distribution. The world model with this stochastic feature fit nicely with participants’ subjective sense of objects’ stability and explained the illusion that taller objects are perceived as more likely to fall. Furthermore, a computational model with reinforcement learning revealed that the stochastic characteristic likely originated from experience-dependent comparisons between predictions formed by internal simulations and the realities observed in the external world, which illustrated the ecological advantage of stochastic representation in balancing accuracy and speed for efficient stability inference. The stochastic world model on gravity provides an example of how a priori knowledge of the physical world is implemented in mind that helps humans operate flexibly in open-ended environments. Significance Statement Humans possess an exceptional capacity for inferring the stability of objects, a skill that has been crucial to the survival of our predecessors and continues to facilitate our daily interactions with the natural world. The present study elucidates that our representation of gravitational direction adheres to a Gaussian distribution, with the vertical orientation as the maximum likelihood. This stochastic representation is likely to have originated from our interactions with the physical world, conferring an ecological advantage of balancing accuracy with speed. Therefore, the world model on gravity in the mind is a distorted replica of the natural world, enabling adaptive functionality in open-ended environments and thus shedding light on developing machines imbued with embodied intelligence.
Gribov copies and the Faddeev–Popov formula in lattice gauge theories

We present a rigorous, nonperturbative derivation of a lattice version of the Faddeev–Popov integral. This derivation shows that Gribov copies can occur in the lattice theory for certain gauges, but these copies do not affect normalized functional integrals in the lattice theory. Furthermore, taking the formal limit as the lattice spacing tends to zero leads to the usual continuum Faddeev–Popov integral.
Personality Prediction from Social Networks: a Review of Works

Today, the potential of social networks for all types of communication is difficult to overestimate. For business communication in virtual communities, it is important to take into account the socio-psychological features of the participants in the communication process. This actualized various aspects of network identity, virtual personality behavior, and online persona. This study offers a review of the scientific literature on personality prediction based on the analysis of different content generated in social networks. First, we analyzed the literature that used methods for analyzing text and photos from social networks using different approaches. The analysis emphasized that in the modern digital age, psychological aspects of communication in social networks and methods of identifying the personality of social network users based on their social activity and the practice of using language and images are very much in demand and relevant. We have proposed a comparison table of existing personality prediction methods based on relevant parameters. In addition, based on the analysis, a program of future research in the field of intellectual analysis of content for the purpose of personality prediction in social networks was determined.
Narrow-band metal-oxide-semiconductor photodetector

Si-based photodetectors for narrow-band ultraviolet light (319 nm) and green light (500 nm) detection are demonstrated using a metal-oxide-semiconductor tunneling structure. By using appropriate selection of gate metal, the metal-oxide-semiconductor tunneling diode can detect specific range of light. Due to the spectral dependence of absorption and reflection of the Ag and Au as gate electrodes, the narrow-band detection of ultraviolet and green light can be achieved, respectively. The photodetectors with 130 nm thick Ag gate and 70 nm thick Au gate exhibit peak responsivities of 5.1 and 0.3 mA/W at 319 and 500 nm, respectively.
Automatic Mobile Video Remixing and Collaborative Watching Systems

In the thesis, the implications of combining collaboration with automation for remix creation are analyzed. We first present a sensor-enhanced Automatic Video Remixing System (AVRS), which intelligently processes mobile videos in combination with mobile device sensor information. The sensor-enhanced AVRS system involves certain architectural choices, which meet the key system requirements (leverage user generated content, use sensor information, reduce end user burden), and user experience requirements. Architecture adaptations are required to improve certain key performance parameters. In addition, certain operating parameters need to be constrained, for real world deployment feasibility. Subsequently, sensor-less cloud based AVRS and low footprint sensorless AVRS approaches are presented. The three approaches exemplify the importance of operating parameter tradeoffs for system design. The approaches cover a wide spectrum, ranging from a multimodal multi-user client-server system (sensor-enhanced AVRS) to a mobile application which can automatically generate a multi-camera remix experience from a single video. Next, we present the findings from the four user studies involving 77 users related to automatic mobile video remixing. The goal was to validate selected system design goals, provide insights for additional features and identify the challenges and bottlenecks. Topics studied include the role of automation, the value of a video remix as an event memorabilia, the requirements for different types of events and the perceived user value from creating multi-camera remix from a single video. System design implications derived from the user studies are presented. Subsequently, sport summarization, which is a specific form of remix creation is analyzed. In particular, the role of content capture method is analyzed with two complementary approaches. The first approach performs saliency detection in casually captured mobile videos; in contrast, the second one creates multi-camera summaries from role based captured content. Furthermore, a method for interactive customization of summary is presented. Next, the discussion is extended to include the role of users’ situational context and the consumed content in facilitating collaborative watching experience. Mobile based collaborative watching architectures are described, which facilitate a common shared context between the participants. The concept of movable multimedia is introduced to highlight the multidevice environment of current day users. The thesis presents results which have been derived from end-to-end system prototypes tested in real world conditions and corroborated with extensive user impact evaluation.
Distributed data & resources: models, tractability, and complexity

There are many examples for the fact that the growth of a system is limited if this system relies on important central instances for supply or control. In a growing system, the central instances turn into bottlenecks, thus making the system inefficient. Examples for this phenomenon can be found in computer science, in history, and even in the behavior of dinosaurs. Distributed systems have great potential to bypass such bottlenecks, but due to ”friction” issues such as incomplete knowledge, we may not be able to exploit their potential. In this thesis we show that some of these issues can be handled quite well in weak and realistic models. More specifically, we present and discuss three examples: 1. Distributing Rare Resources: Roman Domination and Win–Win Given a graph, servers (resources) should be placed on nodes to service a pair of requests that can occur at nodes. Since resources are rare, the number of used resources should be minimized. What is the computational complexity of this problems, and how much control, communication, or interaction is needed to organize the service? We give detailed characterization of the computational complexity of these problems. Especially, we show that these problems are NP–hard; and for Planar Roman Domination, a Polynomial Time Approximation Scheme (PTAS) is presented. 2. Distributed Data Structure Given a distributed system of processors/computers/servers with weak assumptions, is it possible to build and maintain a distributed data structure in this system? We propose a distributed dictionary that supports insert and search operations and that tolerates arbitrary single server crashes. In contrast to other proposals of distributed fault tolerant search structures, our solution works in an asynchronous and weak environmental setting. 3. Distributed Coordination: Point Formation There are n robots in the Euclidean plane that should move to one destination point. What is a minimal set of abilities that the robots have to have in order to complete this task? We define the concept of contraction functions and show that with this concept, the point formation problem can be solved in an asynchronous model. The results show that these problems can be solved in weak and realistic settings. We will discuss these problems individually, but we will discuss the connections between them as well. Interestingly, we will find connections between the point formation problem and facility location as well.
The decomposability of torsion free modules of finite rank

Throughout this paper R will be an integral domain, not a field ; Q will be the quotient field of R; and K will be the i? -module QjR. R will be said to have property D, if every torsion-free i? -module of finite rank is a direct sum of /? -modules of rank one. In [9, §6] I attempted to give necessary and sufficient conditions for an integral domain to have property D. I have since discovered, however, that Lemma 6.4 of that paper is false, with the result that Theorem 6.1 is also false as stated, and needs some rather strong additional hypotheses to be resurrected. Other false lemmas based on Lemma 6.4 are Proposition 6.5 and Corollary 6.7; and Lemma 6.8 remains without a valid proof. Compounding the confusion, I have also discovered an error in Kaplansky's proof of his theorem [4] which purported to handle the Noetherian case, and this theorem remains without a valid proof. Proposition 6.11 and Corollary 6.12 of my paper [9] were based on Kaplansky's proof, and are false as stated. Corollary 6.13 remains without a valid proof. The purpose of this paper is to attempt to restore some order out of this chaos. In Theorem 4 I have settled the Noetherian case. This theorem states that a Noetherian domain has property D if and only if it is one of two types of Noetherian domains. However, I have not been able to find an example of a ring of type (1); i.e. a principal ideal domain R with exactly two nonzero prime ideals Px, P2 and such that RPl, RP2 are complete discrete valuation rings. It was precisely this type of ring that Kaplansky thought that he had proved could not exist. Thus one of the remaining unsolved tasks in finding all of the kinds of integral domains that have property D is either to produce an example of this type of ring, or to prove that it cannot exist. In Theorem 3 I have shown that if R is an /z-local domain with more than one maximal ideal, then R has property D if and only if R has exactly two maximal ideals Mx, M2 and RMl, RM2 are maximal valuation rings. The question of whether such a ring can exist is, of course, a generalization of the previous question raised. Theorem 2 proves that a valuation ring has property D if and only if it is a maximal valuation ring. The major part of this result, namely that a maximal valuation ring has property D, is originally due to Kaplansky [3, Theorem 12] who generalized Priifer's result [11] for complete discrete valuation rings. Both of
Control of Ga Distribution in Cu(In,Ga)Se2 Photovoltaic Absorber by Solid-State Selenizatoin of CuGa/In/Se/In/CuGa Stack

Among many key parameters required to obtain a record-efficiency Cu(In,Ga)Se2 (CIGS) cell, the band-gap of CIGS should have a double-graded profile in which the band-gap increases toward both of the back and front of the absorber. In an effort to obtain an increased Ga content near the junction area which will raise the band-gap energy of CIGS, a novel metal precursor layered with predetermined amount of Se was annealed in N2 ambient. By inserting the Se layer in between metallic precursor layers, it was found that the front band-gap was increased due to the high Ga content by changing the direction of selenization reaction from inside to outside of metallic precursor. The proposed method is expected to provide a simple process for high quality CIGS photovoltaic absorber layer. The conversion efficiency of 6.80% with Jsc = 37.65 mA/cm2, Voc = 0.51 V, and FF= 35.4% in an active area of 0.48 cm2 was achieved.