Miracle-dz/UniFAR-FTUs huggingface dataset:
Not Restricted to the Ends: Yeast Telomere Proteins Rif1 and Cdc13 Function in Double-Strand Break Repair Pathways with Implications for Genome Stability

DNA double-strand breaks (DSBs) are the most lethal form of DNA damage; a single DSB, if left unrepaired, can cause cell death. Inaccurately repaired DSBs are sources of mutations, chromosomal rearrangements and genome instability. Telomeres, TG-rich nucleoprotein structures at the termini of eukaryotic chromosomes, protect chromosome ends from nucleolytic degradation and distinguish chromosome ends from those generated by DSBs. In most eukaryotes, proper telomere maintenance requires a specialized reverse transcriptase, telomerase, that utilizes an enzyme-associated RNA as template for new telomere synthesis. Increasingly, telomere-associated proteins are being recognized as playing roles in the repair of internal DSBs. At endonuclease-induced DSBs immediately preceded by ectopic, short telomere seeds, the telomeric single-stranded DNA binding protein Cdc13 recruits telomerase, promoting the addition of new (de novo) telomere sequences to the telomere seed. However, spontaneous DSBs occur very infrequently and as such, are rarely expected to occur immediately adjacent to telomere-like seed sequences. An experimental system in which a DSB is induced at a distance (~3 kb) from endogenous Sites of de novo Telomere Addition (SiRTAs) in budding yeast was utilized as a more representative model of de novo telomere addition following spontaneous DSBs. These telomere-like SiRTAs incurred high frequencies of de novo telomere addition relative to flanking sequences. Additionally, de novo telomere addition at these SiRTAs required a bipartite structure in which Cdc13 binding to a stimulatory (Stim) sequence strongly stimulates telomere addition at a nearby target (Core) sequence. The role of yet another budding yeast telomere-associated protein, Rif1, in DSB repair was also explored using an experimental system of an endonuclease-induced DSB that is primarily repaired by imprecise non-homologous end joining (NHEJ). Wild-type repair junctions contained only deletions. However, rif1â repair junctions contained relatively smaller deletions, as well as insertions, indicative of ends undergoing less resection in the absence of Rif1. A rif1 mutant lacking the protein phosphatase-1-interacting domain phenocopies the rif1â mutant, implicating this domain in Rif1âs role in regulating the fidelity of DSB repair.
Phytophthora abietivora, A New Species Isolated from Diseased Christmas Trees in Connecticut, U.S.A.

A number of fir species (Abies) are produced as Christmas trees around the world. In particular, Fraser fir (Abies fraseri (Pursh) Poir. ) is popular as it yields high-quality Christmas trees in temperate North America and Europe. A Phytophthora sp. causing root rot on Fraser fir was isolated from a Christmas tree farm in Connecticut, U.S.A. , and found to be new to science according to morphological and molecular phylogenetic analysis using multilocus DNA sequences from ITS, Cox1, β-Tub, Nadh1, and Hsp90 loci. Thus, it was described and illustrated as Phytophthora abietivora. An informative Koch's postulates test revealed that P. abietivora was the pathogen causing root rot of Fraser fir.
Characterization of the complete chloroplast genome of Malus baccata var. xiaojinensis

Abstract Malus baccata var. xiaojinensis belonging to Rosaceae is not only an ornamental tree but also an apple genotype that is highly tolerant to Fe deficiency. In this study, we reported the complete chloroplast (cp) genome of M. baccata var. xiaojinensis using ILLUMINA sequencing. The whole cp genome is 160,067 bp in length, containing a pair of inverted repeats (IRs) of 26,358 bp, a large single copy (LSC) region of 88,157 bp and a small single copy (SSC) region of 19,194 bp. And, the overall GC content of the cp genome was 36.56%. A total of 110 unique genes were found in the cp genome. 17 genes were duplicated in the IRs, including six protein-coding genes, seven tRNA genes, and four rRNA genes. Fourteen genes contained one intron, whereas three genes (rps12, clpP, and ycf3) contained two introns. The phylogenetic analysis demonstrated a close relationship between M. baccata var. xiaojinensis and Malus hupehensis.
Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome using Tandem Mass Tags

Cells respond to environmental perturbations and insults through modulating protein abundance and function. However, the majority of studies have focused on changes in RNA abundance because quantitative transcriptomics has historically been more facile than quantitative proteomics. Modern Orbitrap mass spectrometers now provide sensitive and deep proteome coverage, allowing direct, global quantification of not only protein abundance, but also post-translational modifications (PTMs) that regulate protein activity. We implemented, and validated using the well-characterized heat shock response of budding yeast, a tandem mass tagging (TMT), triple-stage mass spectrometry (MS3) strategy to measure global changes in the proteome during the yeast heat shock response over nine timepoints. We report that basic pH, ultra-high performance liquid chromatography (UPLC) fractionation of tryptic peptides yields superfractions of minimal redundancy, a crucial requirement for deep coverage and quantification by subsequent LC-MS3. We quantified 2,275 proteins across 3 biological replicates, and found that differential expression peaked near 90 minutes following heat shock (with 868 differentially expressed proteins at 5% FDR). The sensitivity of the approach also allowed us to detect changes in the relative abundance of ubiquitination and phosphorylation PTMs over time. Remarkably, relative quantification of post-translationally modified peptides revealed striking evidence of regulation of the heat shock response by protein PTMs. These data demonstrate that the high precision of TMT-MS3 enables peptide-level quantification of samples, which can reveal important regulation of protein abundance and regulatory PTMs under various experimental conditions.
Does REDD+ have a chance? Implications from Pemba, Tanzania

Abstract Conservation scientists continue to debate the strengths and weaknesses of REDD+ as an instrument to slow greenhouse gas emissions in the developing world. We propose that general positions on this debate are less helpful than drawing lessons from specific investigations into the features of individual projects that make them successful or not. Here, focusing on a site-specific REDD+ intervention in Pemba, Zanzibar (Tanzania), we examine the circumstances under which REDD+ has a chance of success, teasing out specific features of both REDD+ interventions and the socio-economic and institutional contexts that render REDD+ a potentially valuable complement to community forestry. Additionally, we highlight some unanticipated positive outcomes associated with the design features of REDD+ projects. Our broader goal is to move away from ideologically-driven debate to empirically-based identification of general conditions where REDD+ could work, and to provide policy recommendations.
Using Call Detail Records of Mobile Network Operators for Transportation Studies

Contemporary transportation research is seeing a steady incline in the use of new, digital tracking data. The necessity for such new types of data has risen from the continuous growth of society’s mobility, the attractiveness of big data, and the need for data that could be collected automatically to be used in developing various monitoring systems. However, introducing new types of data requires the developing and thorough testing of new methodologies. In the current chapter, the authors introduce some methodological issues related to using passive mobile positioning data in transportation research. The Call Detail Records (CDR) and Data Detail Records (DDR) of Mobile Network Operators are a set of data that are automatically recorded and used with increasing frequency by scientists, including transportation researchers and developers of monitoring systems. The authors go on to introduce the Estonian experience in managing such data, spatial and temporal interpolation, the determining of anchor points, and activities responsible for movement. They assess both positive and negative aspects of using passive mobile positioning data and briefly consider legislation and privacy issues in regards to such data.
RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements

Transposons and other repetitive sequences make up a large part of complex genomes. Repetitive sequences can be co-opted into a variety of functions and thus provide a source for evolutionary novelty. However, comprehensively detecting ancestral repeats that align between species is difficult since considering all repeat-overlapping seeds in alignment methods that rely on the seed-and-extend heuristic results in prohibitively high runtimes. Here, we show that ignoring repeat-overlapping alignment seeds when aligning entire genomes misses numerous alignments between repetitive elements. We present a tool – RepeatFiller – that improves genome alignments by incorporating previously-undetected local alignments between repetitive sequences. By applying RepeatFiller to genome alignments between human and 20 other representative mammals, we uncover between 22 and 84 megabases of previously-undetected alignments that mostly overlap transposable elements. We further show that the increased alignment coverage improves the annotation of conserved non-exonic elements, both by discovering numerous novel transposon-derived elements that evolve under constraint and by removing thousands of elements that are not under constraint in placental mammals. In conclusion, RepeatFiller contributes to comprehensively aligning repetitive genomic regions, which facilitates studying transposon co-option and genome evolution. Source code https://github.com/hillerlab/GenomeAlignmentTools
Challenges of Meta Access Control Model Enforcement to an Increased Interoperability

When organizations are collaborating, their access control models need to interoperate. However, there are too many access control model variants, and the interoperability enforcement consumes extra effort. In this context, this chapter identifies the challenges of how to design and enforce a meta-access control model to facilitate the interoperability between the different access control mechanisms available. The problem is posed using an ontological approach. Then, the challenges are explained using a descriptive explanation of the meta access control enforcement. The core issues addressed are access models interoperability, standardization of storage for access data, and provisioning of access models.
Automatic Monitoring and control of Vehicle Entry/Exit In Forest Area with Raspberry-pi, python and open cv

In this paper we propose a completely automated monitoring and control of vehicle entry-exit in restricted area using raspberry pi system. The project aims at designing a system which captures vehicle image along with its number plate automatically and further these details are verified with the database filled in online registration form consist of username, mobile number, vehicle number and full address. Farther the details are authenticated then it is processed by Raspberry Pi to authorise to enter the vehicle in the forest area. Once the information is filled in an online registration form the user gets a four digit random code as the receipt of conformation. That random code will be enter at the time of visiting. On the entrance gate camera capture image of vehicle and from that image the number plate is extracted then that extracted number is verified with the authorised registered number plate number. Raspberry Pi is connected with a server for verification of registered data with the image processing tool OCR. If the verification is susses fully done with the comparison of online registered data base and the extracted number plate number then visitor enter their four digit random code. If the code is match then the gate will be open. When the authorized vehicle was detected then the system operates the gate using DC motor. The system also alerts the authorities when any unauthorized image of number plate was detected using buzzer alarm system and led. The aim of this research is to develop and implement an authorized automatic gate control system that will increase security and convenience at entrance of all restricted forest places that require protection and Security. The auto gate control will be works without manual help and the system will help to recognizes license plates with the authority at entrance gate and take an action to permits the vehicle in a forest area.
Convergence estimates for the Magnus expansion III. Banach--Lie algebras

We review and provide simplified proofs related to the Magnus expansion, and improve convergence estimates. Observations and improvements concerning the Baker--Campbell--Hausdorff expansion are also made. In this Part III, we consider the Banach--Lie algebraic setting. We show how to improve the ``standard'' convergence bound $\boldsymbol\delta= 2.1737374\ldots$ using the customary generating function / ODE methods. Then we discuss how to achieve better convergence bounds using the resolvent method. The emphasis here is on the variety of the methods, rather than pushing them to the extreme. Nevertheless, regarding the cumulative convergence radii, we show how to establish $2.427<\mathrm C_\infty^{\mathrm{Lie}}\leq 4$ for the Magnus expansion, and $2.93<\mathrm C^{\mathrm{Lie}}_2 \leq 4\sqrt2=5.656\ldots$ for the BCH expansion.
The density ratio of generalized binomial versus Poisson distributions

Let $b(x)$ be the probability that a sum of independent Bernoulli random variables with parameters $p_1, p_2, p_3, \ldots \in [0,1)$ equals $x$, where $\lambda := p_1 + p_2 + p_3 + \cdots$ is finite. We prove two inequalities for the maximal ratio $b(x)/\pi_\lambda(x)$, where $\pi_\lambda$ is the weight function of the Poisson distribution with parameter $\lambda$.
The Implementation of Quantum Computing Operations with Phase Modulated Microwave Pulses and High-Spin Ions at Zero Magnetic Fields

New physical implementations of quantum computing elementary operations by pulse manipulations with electron spins of paramagnetic ions having two electrons and spin S=1 in a zero magnetic field are proposed. New type of microwave pulses with variable phases and different polarizations are able to induce different transitions between ion spin states, and those transitions are described by quantum computing operators. To describe the effects of such pulses, a new way to present exponential operators as polynomials of Pauli matrices is proposed.
Quantum optimal transport for approximately finite-dimensional $C^{*}$-algebras

We introduce optimal transport of states on AF-$C^{*}$-algebras, using a dynamic formulation of the metric in the spirit of Benamou-Brenier. Essential for having energy functionals is an extension of quasi-entropies after Hiai and Petz to the approximately finite-dimensional setting compatible with taking conditional expectations. The metric geometry on states is a limit geometry of an ascending chain of metric geometries on state spaces of the finite-dimensional $C^{*}$-algebras generating the AF-$C^{*}$-algebra in question. Using this limit process, we prove equivalence of synthetic lower Ricci bounds and a gradient estimate for unital AF-$C^{*}$-algebras under ergodicity assumptions. The latter are satisfied for examples arising when quantising noncommutative differential geometries, which we show to have non-negative lower Ricci bounds.
A Review of Soft Robots

Traditional robots have rigid links and structures that limit their ability to interact with the dynamics of their immediate environment. For example, conventional robot manipulators with rigid links can only manipulate objects using specific end effectors. These robots often encounter difficulties operating in unstructured and highly congested environments. A variety of biological organisms exhibit complex movement with soft structures devoid of rigid components. Inspired by biology, researchers have been able to design and build soft robots. With a soft structure and redundant degrees of freedom, these robots can be used for delicate tasks in unstructured environments. This review discusses the motivation for soft robots, their design processes as well as their applications and limitations. Soft robots have the ability to operate in unstructured environment due to their inherent potential to exploit morphological computation to adapt to, and interact with, the world in a way that is difficult with rigid systems. Soft robots could be used for operations, ranging from search and rescue operations in a natural disaster relief effort, and of emerging interest is in the field of medical care as seen in personal robots.
Transition from Dirac points to exceptional points in anisotropic waveguides

We uncover the existence of Dirac and exceptional points in waveguides made of anisotropic materials, and study the transition between them. Dirac points in the dispersion diagram appear at propagation directions where the matrix describing the eigenvalue problem for bound states splits into two blocks, sorting the eigenmodes either by polarization or by inner mode symmetry. Introducing a non-Hermitian channel via a suitable leakage mechanism causes the Dirac points to transform into exceptional points connected by a Fermi arc. The exceptional points arise as improper hybrid leaky states and, importantly, are found to occur always out of the anisotropy symmetry planes.
Partial Separability and Functional Graphical Models for Multivariate Gaussian Processes

The covariance structure of multivariate functional data can be highly complex, especially if the multivariate dimension is large, making extensions of statistical methods for standard multivariate data to the functional data setting challenging. For example, Gaussian graphical models have recently been extended to the setting of multivariate functional data by applying multivariate methods to the coefficients of truncated basis expansions. However, a key difficulty compared to multivariate data is that the covariance operator is compact, and thus not invertible. The methodology in this paper addresses the general problem of covariance modelling for multivariate functional data, and functional Gaussian graphical models in particular. As a first step, a new notion of separability for the covariance operator of multivariate functional data is proposed, termed partial separability, leading to a novel Karhunen–Loève-type expansion for such data. Next, the partial separability structure is shown to be particularly useful in order to provide a well-defined functional Gaussian graphical model that can be identified with a sequence of finite-dimensional graphical models, each of identical fixed dimension. This motivates a simple and efficient estimation procedure through application of the joint graphical lasso. Empirical performance of the method for graphical model estimation is assessed through simulation and analysis of functional brain connectivity during a motor task.
Enhancement of optical coherence in $^{167}$Er:Y$_2$SiO$_5$ crystal at sub-Kelvin temperatures.

Er:YSO crystal is promising candidate with great variety of its potential applications in quantum information processing and quantum communications ranging from optical/microwave quantum memories to circuit QED and microwave-to-optics frequency converters. Some of the above listed applications require ultra-low temperature environment, i.e. temperatures $T\lesssim0.1~$K. Most of the experiments with erbium doped crystals have been so far carried out at temperatures above 1.5 K. Therefore, only little information is known about Er:YSO coherence properties at millikelvins. Here, we investigate optical decoherence of $^{167}$Er:Y$_2$SiO$_5$ crystal by performing 2- and 3-pulse echo experiments at sub-Kelvin temperature range and at weak and moderate magnetic fields. We show that the deep freezing of the crystal results in an increase of optical coherence time by one order of magnitude below 1.5 Kelvin at the field of $\sim$0.2 T. We further describe the detailed investigation of the decoherence mechanisms in this regime.
Generating valid Euclidean distance matrices

Generating point clouds, e.g., molecular structures, in arbitrary rotations, translations, and enumerations remains a challenging task. Meanwhile, neural networks utilizing symmetry invariant layers have been shown to be able to optimize their training objective in a data-efficient way. In this spirit, we present an architecture which allows to produce valid Euclidean distance matrices, which by construction are already invariant under rotation and translation of the described object. Motivated by the goal to generate molecular structures in Cartesian space, we use this architecture to construct a Wasserstein GAN utilizing a permutation invariant critic network. This makes it possible to generate molecular structures in a one-shot fashion by producing Euclidean distance matrices which have a three-dimensional embedding.
Affine-null formulation of the gravitational equations: Spherical case

A new evolution algorithm for the characteristic initial value problem based upon an affine parameter rather than the areal radial coordinate used in the Bondi-Sachs formulation is applied in the spherically symmetric case to the gravitational collapse of a massless scalar field. The advantages over the Bondi-Sachs version are discussed, with particular emphasis on the application to critical collapse. Unexpected quadratures lead to a simple evolution algorithm based upon ordinary differential equations which can be integrated along the null rays. For collapse to a black hole in a Penrose compactified spacetime, these equations are regularized throughout the exterior and interior of the horizon up to the final singularity. They are implemented as a global numerical evolution code based upon the Galerkin method. New results regarding the global properties of critical collapse are presented.
Soft wearable assistive robotics: exosuits and supernumerary limbs

The intrinsic soft nature of compliant supernumerary limbs and exosuits makes them appealing candidates for assisting human movements, with potential applications in healthcare, human augmentation and logistics. In the following chapter, we describe the technology used in exosuits and supernumerary limbs for assistance of activities of daily living, with emphasis on aiding grasping and flexion/ extension of the elbow joint. We discuss the mechanical design principles of such devices, detail the control paradigms that can be used for intention-detection and present the design and evaluation of cutaneous interfaces used for force feedback rendering. Tests on healthy and impaired subjects highlight that exosuits and supernumerary limbs are potential cost-effective and intrinsically safe solutions for increasing the capabilities of healthy subjects and improving the quality of life of subjects suffering from motor disorders.
High-fidelity entangling gates for quantum-dot hybrid qubits based on exchange interactions

Quantum dot hybrid qubits exploit an extended charge-noise sweet spot that suppresses dephasing and has enabled the experimental achievement of high-fidelity single-qubit gates. However, current proposals for two-qubit gates require tuning the qubits away from their sweet spots. Here, we propose a two-hybrid-qubit coupling scheme, based on exchange interactions, that allows the qubits to remain at their sweet spots at all times. The interaction is controlled via the inter-qubit tunnel coupling. By simulating such gates in the presence of realistic quasistatic and $1\! /\! f$ charge noise, we show that our scheme should enable controlled-$Z$ gates of length $\sim$5~ns, and Z-CNOT gates of length $\sim$7~ns, both with fidelities $>$99.9\%.