Miracle-dz/UniFAR-FTUs huggingface dataset:
The substrate specificity of the human ADP/ATP carrier AAC1

Abstract The mitochondrial ADP/ATP carrier imports ADP from the cytosol into the mitochondrial matrix for its conversion to ATP by ATP synthase and exports ATP out of the mitochondrion to replenish the eukaryotic cell with chemical energy. Here the substrate specificity of the human mitochondrial ADP/ATP carrier AAC1 was determined by two different approaches. In the first the protein was functionally expressed in Escherichia coli membranes as a fusion protein with maltose binding protein and the effect of excess of unlabeled compounds on the uptake of [32P]-ATP was measured. In the second approach the protein was expressed in the cytoplasmic membrane of Lactococcus lactis. The uptake of [14C]-ADP in whole cells was measured in the presence of excess of unlabeled compounds and in fused membrane vesicles loaded with unlabeled compounds to demonstrate their transport. A large number of nucleotides were tested, but only ADP and ATP are suitable substrates for human AAC1, demonstrating a very narrow specificity. Next we tried to understand the molecular basis of this specificity by carrying out molecular-dynamics simulations with selected nucleotides, which were placed at the entrance of the central cavity. The binding of the phosphate groups of guanine and adenine nucleotides is similar, yet there is a low probability for the base moiety to be bound, likely to be rooted in the greater polarity of guanine compared to adenine. AMP is unlikely to engage fully with all contact points of the substrate binding site, suggesting that it cannot trigger translocation.
Polar Invasion and Translocation of Neisseria meningitidis and Streptococcus suis in a Novel Human Model of the Blood-Cerebrospinal Fluid Barrier

Acute bacterial meningitis is a life-threatening disease in humans. Discussed as entry sites for pathogens into the brain are the blood-brain and the blood-cerebrospinal fluid barrier (BCSFB). Although human brain microvascular endothelial cells (HBMEC) constitute a well established human in vitro model for the blood-brain barrier, until now no reliable human system presenting the BCSFB has been developed. Here, we describe for the first time a functional human BCSFB model based on human choroid plexus papilloma cells (HIBCPP), which display typical hallmarks of a BCSFB as the expression of junctional proteins and formation of tight junctions, a high electrical resistance and minimal levels of macromolecular flux when grown on transwell filters. Importantly, when challenged with the zoonotic pathogen Streptococcus suis or the human pathogenic bacterium Neisseria meningitidis the HIBCPP show polar bacterial invasion only from the physiologically relevant basolateral side. Meningococcal invasion is attenuated by the presence of a capsule and translocated N. meningitidis form microcolonies on the apical side of HIBCPP opposite of sites of entry. As a functionally relevant human model of the BCSFB the HIBCPP offer a wide range of options for analysis of disease-related mechanisms at the choroid plexus epithelium, especially involving human pathogens.
Multilabel Classiﬁcation of Drug-like Molecules via Max-margin Conditional Random Fields

We present a multilabel learning approach for molecular classiﬁcation, an important task in drug discovery. We use a conditional random ﬁeld to model the dependencies between drug targets and discriminative training to separate correct multilabels from incorrect ones with a large margin. Eﬃcient training of the model is ensured by conditional gradient optimization on the marginal dual polytope, using loopy belief propagation to ﬁnd the steepest feasible ascent directions. In our experiments, the MMCRF method outperformed the support vector machine with state-of-the-art graph kernels on a dataset comprising of cancer inhibition potential of drug-like molecules against a large number cancer cell lines.
Rare Earth Element Behavior in Zircon-Melt Systems

Natural zircon crystals incorporate rare earth elements (REE) into their structure at concentrations determined by the pressure, temperature, and composition of their growth environment. In principle, REE concentrations in magmatic zircon crystals can be used to infer their conditions of growth and the composition of the melt from which they grew—provided accurate information is available about the distribution of REE between zircon and melt. Currently available zircon-melt partitioning data show a range in values covering several orders of magnitude for some REE. Further experimental work and studies using carefully selected natural samples are required to fully understand REE incorporation in zircon.
The relationship between total precipitable water and surface‐level humidity over the sea surface: A further evaluation

The fifth-order polynomial regression relating total precipitable water (W) and surface-level humidity (Q) over the sea surface, proposed by Liu (1986), has been further verified by instantaneous radiosonde ascents from 13 experiments conducted in geographically different regions ranging from the equatorial Pacific to the Norwegian Sea. When Q ranges from 3 to 21 g/kg, the composite root-mean-square-error between Liu's formula and these 13 experiments is found to be approximately 1 g/kg. It is therefore suggested that as a first approximation, Liu's formula may be useful for operational weather analysis and forecasting using instantaneous data, inasmuch as Q can be determined with W measured routinely worldwide by satellites.
Tropical Artisanal Coastal Fisheries: Challenges and Future Directions

Artisanal fisheries occur all over the tropics and provide an important source of protein and income for many coastal communities. However, varied types and magnitudes of anthropogenic impacts threaten the environmental, economic, and socio-cultural sustainability of this poorly studied fishing practice. This article reviews the scattered literature on tropical artisanal coastal fisheries, identifying key challenges to ensure future sustainability. Despite huge data shortfalls, there is considerable evidence that artisanal fisheries have a significant influence on the distribution and abundance of target and by-catch species, in addition to wider impacts on biodiversity, biomass, assemblage structure, community dynamics, and ecosystem functioning. Despite these immediate and considerable threats, regulation and management of artisanal fisheries are problematic. Local communities in the coastal tropics are frequently very poor, and families frequently rely on fishing for food security and income. Ensuring social and environmental sustainability therefore entails models of governance that are able to adaptively manage these complex socio-ecological systems. Such models are being developed, but it is unclear whether there are sufficient resources and technical capacity to widely implement them before the widespread collapse of fisheries with potentially serious consequences for the communities that rely on them.
Long-Range Visual Homing

A biologically-inspired approach to robot route following is presented. Snapshot images of a robot's environment are captured while learning a route. Later, when retracing the route, the robot uses visual homing to move between positions where snapshot images had been captured. This general approach was inspired by experiments on route following in wood ants. The impact of odometric error and another key parameter is studied in relation to the number of snapshots captured by the learning algorithm. Tests in a photo-realistic simulated environment reveal that route following can succeed even on relatively sparse paths. A major change in illumination reduces, but does eliminate, the robot's ability to retrace a route.
A novel hardware algorithm for real-time image recognition based on real AdaBoost classification

Real-time object detection is important for surveillance applications. This paper describes a high-performance object detector using a commercially available FPGA. Major bottlenecks in the real AdaBoost classifier are resolved. A new FIR-filter-like hardware architecture takes advantage of an FPGA's hardware parallelism and block-RAM structure. The resulting design uses Xilinx Virtex 5 and achieves the real-time processing performance of 220 f/s at 201 MHz and adjustable recognition performance with a variable number of weak classifiers. This is the first demonstration of a histogram of oriented gradients and Real AdaBoost detector on an FPGA.
Constraint-based Temporal Reasoning with Preferences

Often we need to work in scenarios where events happen over time and preferences are associated to event distances and durations. Soft temporal constraints allow one to describe in a natural way problems arising in such scenarios. In general, solving soft temporal problems require exponential time in the worst case, but there are interesting subclasses of problems which are polynomially solvable. In this paper we identify one of such subclasses giving tractability results. Moreover, we describe two solvers for this class of soft temporal problems, and we show some experimental results. The random generator used to build the problems on which tests are performed is also described. We aiso compare the two solvers highiighting the tradeoE between performance and robustness. Sometimes, however, temporal local preferences are difficult to set, and it may be easier instead to associate preferences to some complete solutions of the problem. To model everything in a uniform way via local preferences only, and also to take advantage of the existing constraint solvers which exploit only local preferences, we show that machine learning techniques can be useful in this respect. In particular, we present a learning module based on a gradient descent technique which induces local temporal preferences from global ones. We also show the behavior of the learning module on randomly-generated examples.
Pairwise Clustering and Graphical Models

Significant progress in clustering has been achieved by algorithms that are based on pairwise affinities between the datapoints. In particular, spectral clustering methods have the advantage of being able to divide arbitrarily shaped clusters and are based on efficient eigenvector calculations. However, spectral methods lack a straightforward probabilistic interpretation which makes it difficult to automatically set parameters using training data. In this paper we use the previously proposed typical cut framework for pairwise clustering. We show an equivalence between calculating the typical cut and inference in an undirected graphical model. We show that for clustering problems with hundreds of datapoints exact inference may still be possible. For more complicated datasets, we show that loopy belief propagation (BP) and generalized belief propagation (GBP) can give excellent results on challenging clustering problems. We also use graphical models to derive a learning algorithm for affinity matrices based on labeled data.
Polar Codes for Cooperative Relaying

We consider the symmetric discrete memoryless relay channel with orthogonal receiver components and show that polar codes are suitable for decode-and-forward and compress-and-forward relaying. In the first case we prove that polar codes are capacity achieving for the physically degraded relay channel; for stochastically degraded relay channels our construction provides an achievable rate. In the second case we construct sequences of polar codes that achieve the compress-and-forward rate by nesting polar codes for source compression into polar codes for channel coding. In both cases our constructions inherit most of the properties of polar codes. In particular, the encoding and decoding algorithms and the bound on the block error probability O(2-Nβ) which holds for any 0<;β<;1/2.
Three theorems in discrete random geometry

These notes are focused on three recent results in discrete ran- dom geometry, namely: the proof by Duminil-Copin and Smirnov that the connective constant of the hexagonal lattice is p 2 + √ 2; the proof by the author and Manolescu of the universality of inhomogeneous bond percola- tion on the square, triangular, and hexagonal lattices; the proof by Beffara and Duminil-Copin that the critical point of the random-cluster model on Z 2 is √ q/(1 + √ q). Background information on the relevant random pro- cesses is presented on route to these theorems. The emphasis is upon the communication of ideas and connections as well as upon the detailed proofs. AMS 2000 subject classifications: Primary 60K35; secondary 82B43. Keywords and phrases: Self-avoiding walk, connective constant, per- colation, random-cluster model, Ising model, star-triangle transformation, Yang-Baxter equation, critical exponent, universality, isoradiality.
The Arabidopsis Chaperone J3 Regulates the Plasma Membrane H+-ATPase through Interaction with the PKS5 Kinase[C][W]

This work examines the effect of a DnaJ homolog, Arabidopsis J3, on the activity of the plasma membrane H+-ATPase, showing that J3 affects activity of the ATPase by direct interaction with and inactivation of a repressor protein kinase, Salt Overly Sensitive2-Like Protein Kinase5. The plasma membrane H+-ATPase (PM H+-ATPase) plays an important role in the regulation of ion and metabolite transport and is involved in physiological processes that include cell growth, intracellular pH, and stomatal regulation. PM H+-ATPase activity is controlled by many factors, including hormones, calcium, light, and environmental stresses like increased soil salinity. We have previously shown that the Arabidopsis thaliana Salt Overly Sensitive2-Like Protein Kinase5 (PKS5) negatively regulates the PM H+-ATPase. Here, we report that a chaperone, J3 (DnaJ homolog 3; heat shock protein 40-like), activates PM H+-ATPase activity by physically interacting with and repressing PKS5 kinase activity. Plants lacking J3 are hypersensitive to salt at high external pH and exhibit decreased PM H+-ATPase activity. J3 functions upstream of PKS5 as double mutants generated using j3-1 and several pks5 mutant alleles with altered kinase activity have levels of PM H+-ATPase activity and responses to salt at alkaline pH similar to their corresponding pks5 mutant. Taken together, our results demonstrate that regulation of PM H+-ATPase activity by J3 takes place via inactivation of the PKS5 kinase.
An Efficient Hardware Implementation of a Robust and Low-Complexity ADSRC Timing Synchronization Design

In this paper, a robust, low-complexity timing synchronization algorithm suitable for 5.9 GHz advanced dedicated short range communications (ADSRC) system and its efficient hardware implementation is proposed. Cross-correlation technique is used to detect the starting point of short training symbol and the guard interval of the long training symbol. The design is implemented in a Xilinx Vertex-II XC2V2000 field programmable gate array (FPGA). Synchronization Error Rate results of Matlab and post-layout simulation show that the proposed algorithm is robust and efficient in high-mobility environments.
A distributed certificate management system (DCMS) supporting group-based access controls

Mainly for scalability reasons, many cryptographic security protocols make use of public key cryptography and require the existence of a corresponding public key infrastructure (PKI). A PKI, in turn, consists of one or several certification authorities (CAs) that issue and revoke certificates for users and other CAs. Contrary to its conceptual simplicity, the establishment and operational maintenance of a CA or PKI has aimed our to be difficult in practice. As a viable alternative, this paper proposes an architecture for a distributed certificate management system (DCMS) that can also be used to provide support for group-based access controls. The architecture has been prototyped and is being used by the Swiss Federal Strategy Unit for Information Technology (FSUIT) to protect access to intranet resources.
Disentangling the Common Variance of Perfectionistic Strivings and Perfectionistic Concerns: A Bifactor Model of Perfectionism

Perfectionism nowadays is frequently understood as a multidimensional personality trait with two higher-order dimensions of perfectionistic strivings and perfectionistic concerns. While perfectionistic concerns are robustly found to correlate with negative outcomes and psychological malfunctioning, findings concerning the outcomes of perfectionistic strivings are inconsistent. There is evidence that perfectionistic strivings relate to psychological maladjustment on the one hand but to positive outcomes on the other hand as well. Moreover, perfectionistic strivings and perfectionistic concerns frequently showed substantial overlap. These inconsistencies of differential relations and the substantial overlap of perfectionistic strivings and perfectionistic concerns raise questions concerning the factorial structure of perfectionism and the meaning of its dimensions. In this study, several bifactor models were applied to disentangle the common variance of perfectionistic strivings and perfectionistic concerns at the item level using Hill et al.’s (2004) Perfectionism Inventory (PI). The PI measures a broad range of perfectionism dimensions by four perfectionistic strivings and four perfectionistic concerns subscales. The bifactor-(S – 1) model with one general factor defined by concern over mistakes as the reference facet, four specific perfectionistic strivings factors, and three specific perfectionistic concerns factors showed acceptable fit. The results revealed a clear separation between perfectionistic strivings and perfectionistic concerns, as the general factor represented concern over mistakes, while the perfectionistic strivings factors each explained a substantial amount of reliable variance independent of the general factor. As a result, factor scores of the specific perfectionistic strivings factors and the general factor had differential relationships with achievement motivation, neuroticism, conscientiousness, and self-efficacy that met with theoretical expectations, while results for manifest subscale scores were ambiguous. Our results question the existence of reliable sub-constructs of perfectionistic concerns independent of the general factor when defined by concern over mistakes.
A Hospice Rotation for Military Medical Residents: A Mixed Methods, Multi-Perspective Program Evaluation.

BACKGROUND An estimated 6,000 to 18,000 additional hospice and palliative medicine (HPM) physicians are needed in the United States. A source could be the military graduate medical education system where 15% of U.S. medical residents are trained. A community-based hospice and palliative care organization created a one-week rotation for military residents including participation in interdisciplinary group visits at patients' homes, facilities, and an inpatient hospice unit. OBJECTIVE Our goal was to evaluate the effectiveness of a one-week community HPM rotation for military medical residents. METHODS A mixed-methods, multi-stakeholder perspective program evaluation model was used for program years 2011 to 2013. Data were managed and analyzed using Microsoft Excel and Atlas.ti. Participants in the rotation were residents training at two local military hospitals. Program evaluation data were collected from residents, military program liaisons, and hospice clinical preceptors. Quantitative data included pre- and post-tests based on Accreditation Council for Graduate Medical Education competencies completed by residents. Qualitative data included resident essays and semi-structured interviews with hospice preceptors and military program liaisons. RESULTS Quantitative and qualitative data suggested that the rotation increased military residents' knowledge, attitudes, and comfort level with HPM. Quantitative analysis of test scores indicated improvements from pre- to post-tests in each of five areas of learning. Qualitative data indicated the rotation created a greater appreciation for the overall importance of HPM and increased understanding of eligibility and methods for pain and symptom management. CONCLUSIONS A one-week community hospice rotation for medical military residents impacts participant's knowledge of and attitudes toward HPM.
Role of glaciohydraulic supercooling in the formation of stratified facies basal ice: Svínafellsjökull and Skaftafellsjökull, southeast Iceland

Cook, S. J., Robinson, Z. P., Fairchild, I. J., Knight, P. G. , Waller, R. I. & Boomer, I. 2009: Role of glaciohydraulic supercooling in the formation of stratified facies basal ice: Svínafellsjökull and Skaftafellsjökull, southeast Iceland. Boreas, 10.1111/j.1502‐3885.2009. 00112.x. ISSN 0300‐9483.
Designing Security for In-vehicle Networks: A Body Control Module (BCM) Centered Viewpoint

The overabundance of attacks reported on in-vehicle networks triggered reactions from both the academic research communities and industry professionals. However, designing security for in-vehicle networks is a challenging task and it is yet unclear to what extent current proposals are suitable for real world vehicles. In this work, we advocate the use of a top-down approach in which we analyze the functionalities along with reported attacks. Due to the abundance of in-vehicle services and the associated large number of Electronic Control Units (ECUs), we center our analysis on a key subsystem from the car: the Body Control Module (BCM). The rationale behind choosing this particular module comes from at least three key factors: i) a large number of components that aredirectly linked to the BCM were target of previously reported attacks (e.g., keys and electronic immobilizes, tire sensors, diagnostic ports, etc.), ii) by design, body components are generally exposed to the outside and it is reasonable to assumethat adversaries will frequently have access to peripherals controlled by the BCM, iii) the BCM controls subsystems thatare both attractive from an economic perspective (e.g., accessto the car), or from a safety perspective (e.g., seat-belts, lights, etc.). Our discussion is entailed by a concrete analysis of therisks of reported attacks and preferable security designs.
Efficient and perfect state transfer in quantum chains

We present a communication protocol for chains of permanently coupled qubits which achieves perfect quantum state transfer and which is efficient with respect to the number of chains employed in the scheme. The system consists of M uncoupled identical quantum chains. Local control (gates, measurements) is only allowed at the sending/receiving end of the chains. Under a quite general hypothesis on the interaction Hamiltonian of the qubits, a theorem is proved which shows that the receiver is able to asymptotically recover the messages by repetitive monitoring of his qubits.
Sampling BSSRDFs with non-perpendicular incidence

Sub-surface scattering is key to our perception of translucent materials. Models based on diffusion theory are used to render such materials in a realistic manner by evaluating an approximation of the material BSSRDF at any two points of the surface. Under the assumption of perpendicular incidence, this BSSRDF approximation can be tabulated over 2 dimensions to provide fast evaluation and importance sampling. However, accounting for non-perpendicular incidence with the same approach would require to tabulate over 4 dimensions, making the model too large for practical applications. In this report, we present a method to efficiently evaluate and importance sample the multi-scattering component of diffusion based BSSRDFs for non-perpendicular incidence. Our approach is based on tabulating a compressed angular model of Photon Beam Diffusion. We explain how to generate, evaluate and sample our model. We show that 1 MiB is enough to store a model of the multi-scattering BSSRDF that is within $0.5\%$ relative error of Photon Beam Diffusion. Finally, we present a method to use our model in a Monte Carlo particle tracer and show results of our implementation in PBRT.