Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of retromer recruitment to endosomes by sequential action of Rab5 and Rab7

The retromer complex mediates retrograde transport of transmembrane cargo from endosomes to the trans-Golgi network (TGN). Mammalian retromer is composed of a sorting nexin (SNX) dimer that binds to phosphatidylinositol 3-phosphate–enriched endosomal membranes and a vacuolar protein sorting (Vps) 26/29/35 trimer that participates in cargo recognition. The mammalian SNX dimer is necessary but not sufficient for recruitment of the Vps26/29/35 trimer to membranes. In this study, we demonstrate that the guanosine triphosphatase Rab7 contributes to this recruitment. The Vps26/29/35 trimer specifically binds to Rab7–guanosine triphosphate (GTP) and localizes to Rab7-containing endosomal domains. Interference with Rab7 function causes dissociation of the Vps26/29/35 trimer but not the SNX dimer from membranes. This blocks retrieval of mannose 6-phosphate receptors to the TGN and impairs cathepsin D sorting. Rab5-GTP does not bind to the Vps26/29/35 trimer, but perturbation of Rab5 function causes dissociation of both the SNX and Vps26/29/35 components from membranes through inhibition of a pathway involving phosphatidylinositol 3-kinase. These findings demonstrate that Rab5 and Rab7 act in concert to regulate retromer recruitment to endosomes.
Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae

ABSTRACT Giant viruses are protist-associated viruses belonging to the proposed order Megavirales; almost all have been isolated from Acanthamoeba spp. Their isolation in humans suggests that they are part of the human virome. Using a high-throughput strategy to isolate new giant viruses from their original protozoan hosts, we obtained eight isolates of a new giant viral lineage from Vermamoeba vermiformis, the most common free-living protist found in human environments. This new lineage was proposed to be the faustovirus lineage. The prototype member, faustovirus E12, forms icosahedral virions of ≈200 nm that are devoid of fibrils and that encapsidate a 466-kbp genome encoding 451 predicted proteins. Of these, 164 are found in the virion. Phylogenetic analysis of the core viral genes showed that faustovirus is distantly related to the mammalian pathogen African swine fever virus, but it encodes ≈3 times more mosaic gene complements. About two-thirds of these genes do not show significant similarity to genes encoding any known proteins. These findings show that expanding the panel of protists to discover new giant viruses is a fruitful strategy. IMPORTANCE By using Vermamoeba, a protist living in humans and their environment, we isolated eight strains of a new giant virus that we named faustovirus. The genomes of these strains were sequenced, and their sequences showed that faustoviruses are related to but different from the vertebrate pathogen African swine fever virus (ASFV), which belongs to the family Asfarviridae. Moreover, the faustovirus gene repertoire is ≈3 times larger than that of ASFV and comprises approximately two-thirds ORFans (open reading frames [ORFs] with no detectable homology to other ORFs in a database).
InSAR analysis of natural recharge to define structure of a ground‐water basin, San Bernardino, California

Using interferometric synthetic aperture radar (InSAR) analysis of ERS‐1 and ERS‐2 images, we detect several centimeters of uplift during the first half of 1993 in two areas of the San Bernardino ground‐water basin of southern California. This uplift correlates with unusually high runoff from the surrounding mountains and increased ground‐water levels in nearby wells. The deformation of the land surface identifies the location of faults that restrict ground‐water flow, maps the location of recharge, and suggests the areal distribution of fine‐grained aquifer materials. Our preliminary results demonstrate that naturally occurring runoff and resultant recharge can be used with interferometric deformation mapping to help define the structure and important hydrogeologic features of a ground‐water basin. This approach may be particularly useful in investigations of remote areas with scant ground‐based hydrogeologic data.
Multi-Target Machine Translation with Multi-Synchronous Context-free Grammars

We propose a method for simultaneously translating from a single source language to multiple target languages T1, T2, etc. The motivation behind this method is that if we only have a weak language model for T1 and translations in T1 and T2 are associated, we can use the information from a strong language model over T2 to disambiguate the translations in T1, providing better translation results. As a specific framework to realize multi-target translation, we expand the formalism of synchronous context-free grammars to handle multiple targets, and describe methods for rule extraction, scoring, pruning, and search with these models. Experiments find that multi-target translation with a strong language model in a similar second target language can provide gains of up to 0.8-1.5 BLEU points. 1
Vulvovaginal Chronic Graft-Versus-Host Disease With Allogeneic Hematopoietic Stem Cell Transplantation

OBJECTIVE: To describe the diagnosis and management of female genital chronic graft-versus-host (GVH) disease, a complication of hematopoietic stem cell transplantation. METHODS: From 1999 to 2006, 33 women with vulvar symptoms or undergoing systematic evaluation for chronic GVH disease were referred 267 (median, range 29–6,117) days after transplantation for gynecologic evaluation. Pertinent histories, laboratory tests, and skin and genital area–directed examinations were performed. Vulvar disease was treated with superpotent topical glucocorticoids and topical estrogen. Sexually active, menopausal women used vaginal dilators, topical glucocorticoids and estrogen, and estrogen vaginal rings for vaginal synechiae. RESULTS: At presentation, most patients complained of vulvar pain during urination and pain that prevented sexual intercourse. Twenty-nine of 33 presenting with vulvovaginal chronic GVH disease had vulvar erythema, with additional signs including vulvar vestibulitis syndrome (n=9), vulvar erosions (n=12), vulvar scarring (n=2), and vaginal scarring (n=6); over time, eight additional patients developed vaginal scarring. Topical glucocorticoids improved vulvar symptoms, and estrogen decreased vulvar mucosal friability. Eleven of 12 patients, who wanted to resume having intercourse, responded to nonsurgical treatment for vaginal synechiae. CONCLUSION: A combination of topical superpotent glucocorticoids and estrogen was effective in the treatment of vulvovaginal chronic GVH disease. In those with vaginal scarring, use of a vaginal dilator and estrogen ring was helpful. Early identification and treatment of vulvovaginal chronic GVH disease ameliorates vulvar pain by healing eroded vulvar mucosa and may prevent the need for surgery for hematocolpos. LEVEL OF EVIDENCE: III
A finite step adaptive implementation of the Pisarenko's harmonic retrieval method in colored noise

An adaptive spectral analysis technique is presented for estimating complex frequencies in colored noise. It is assumed that the noise covariance matrix of the colored noise is known. The method presented in this paper is similar to Thompson's technique of an on line estimation of the eigenvector of the covariance matrix corresponding to the minimum eigenvalue, without explicitly evaluating the covariance matrix. The method of conjugate gradient has been utilized to obtain the eigenvector corresponding to the minimum eigenvalue. The advantages of this technique over the method of steepest descent is that it is a finite step iterative method and secondly there is no arbitrary constants in the expression which dictates the overall rate of convergence. In the proposed method, the spread of the eigenvalues has no significant effect on the overall rate of convergence. The disadvantage of this technique is that one has to store a matrix of data instead of one row only, as is conventionally done. The proposed method however yields unbiased estimates for the frequencies in colored noise.
Turnbull ’ s Nonparametric Estimator for Interval-Censored Data

In most applications, the data may be interval-censored. By interval-censored data, we mean that a random variable of interest is known only to lie in an interval, instead of being observed exactly. In such cases, the only information we have for each individual is that their event time falls in an interval, but the exact time is unknown. A nonparametric estimate of the survival function can also be found in such intervalcensored situations. The survival function is perhaps the most important function in medical and health studies. In this work we describe and illustrate the iterative procedure proposed by Turnbull (1976) to estimate such function. This procedure has been implemented in the software R and the code used is provided in this work.
Rifampicin Alleviates Atopic Dermatitis-Like Response in vivo and in vitro

Atopic dermatitis (AD) is a common inflammatory skin disorder mediated by inflammatory cells, such as macrophages and mast cells. Rifampicin is mainly used for the treatment of tuberculosis. Recently, it was reported that rifampicin has anti-inflammatory and immune-suppressive activities. In this study, we investigated the effect of rifampicin on atopic dermatitis in vivo and in vitro. AD was induced by treatment with 2, 4-dinitrochlorobenzene (DNCB) in NC/Nga mice. A subset of mice was then treated with rifampicin by oral administration. The severity score and scratching behavior were alleviated in the rifampicin-treated group. Serum immunoglobulin E (IgE) and interleukin-4 (IL-4) levels were also ameliorated in mice treated with rifampicin. We next examined whether rifampicin has anti-atopic activity via suppression of mast cell activation. Rifampicin suppressed the release of β-hexosaminidase and histamine from human mast cell (HMC)-1 cultures stimulated with compound 48/80. Treatment with rifampicin also inhibited secretion of inflammatory mediators, such tumor necrosis factor-α (TNF-α) and prostaglandin D2 (PGD2), in mast cells activated by compound 48/80. The mRNA expression of cyclooxygenase 2 (COX-2) was reduced in the cells treated with rifampicin in a concentration-dependent manner. These results suggest that rifampicin can be used to treat atopic dermatitis.
Optimal Conservation of Nature : Estimating Marginal Costs and Benefits of Protecting Endangered Habitat in Finland

What is the optimal level of nature conservation? Although Samuelson’s theory of public goods is deep-rooted and also empirical and conceptual analyses of different aspects of environmental protection are abundant, studies that estimate both marginal benefits and costs of environmental protection are lacking. This study first estimates the marginal costs and benefits of protecting endangered habitat in Finland. The constructed supply and demand of environmental protection are then combined so that different policy alternatives can be assessed. Both costand benefit analyses use direct preference elicitation methods. Marginal costs and benefits are estimable and plausible, and their combination strikingly resembles a textbook example of supply and demand. The estimated “optimal” level of conservation is identified within the sample.
Compact Quasi-Isotropic Dielectric Resonator Antenna With Small Ground Plane

The quasi-isotropic dielectric resonator antenna (DRA) is investigated for the first time. It uses a small ground plane which also serves as an electric dipole. The electric dipole combines with the equivalent magnetic dipole of the DRA to generate quasi-isotropic fields. A choke (balun) is connected to the outer conductor of the coaxial cable to suppress stray radiation. ANSYS HFSS was used to simulate the antenna, and a prototype operating at 2.4-GHz WLAN band was fabricated to verify the simulation. Results show that the difference between the measured maximum and minimum radiation power densities is 5.6 dB over the entire pseudo spherical radiating surface. By using a narrower ground plane and a higher dielectric constant, the gain difference can be reduced to 3.4 dB, approaching the theoretical limit of 3 dB.
BIOCHEMICAL CONSTITUTION OF MAMMALIAN MITOCHONDRIA

Almost 20 years have passed since the isolation of mitochondria from guinea pig liver was announced by Bensley and Hoerr (6) in 1934. This important discovery remained largely unexploited until the researches of Claude on the particulate components of cytoplasm were begun some 5-6 years later. Although Claude at first mistook the mitochondria for secretion granules (17), his methods for the isolation of these cell organelles, which were the first to be described in the literature (17, 19, 20), laid the foundations for the large amount of research on mitochondria that has been carried out in the last few years. The recognition of the key role played by the mitochondrion in the metabolism of the cell is largely the result of the localisation of a number of important enzymatic functions in isolated mitochondria (cf. 97). These enzymatic activities have not merely been detected in isolated mitochondria but, in many cases, have been shown to account for 50 per cent or more of the total cellular activity. The ability to recover large fractions of the total enzyme activity in isolated mitochondria and to demonstrate concentration of this activity in mitochondria indicated to us that the findings were accurate from the cytochemical standpoint. On the other hand, we have hesitated to attach cytochemical significance to the presence of small percentages of the total tissue enzyme activity in mitochondna or in any other subcellular structure, since such results could very readily be the result of adsorption, contamination, or other factors which could not be satisfactorily proved or disproved. Even in those cases in which it has been possible to demonstrate almost exclusive localisation of a cellular function in mitochondria, the possibility of artifacts has always been considered and we have sought and welcomed the appearance of independent methods that would either support or deny the results obtained with isolated mitochondria. Although some such evidence has been reported in support of the localisation of certain enzymes in mitochondria (3, 11), confirmation of the results of the cell fractionation technic has not kept pace with new results obtained with this method. It is hoped that this situation will be corrected in the future.
Expression and RNA Interference of Ribosomal Protein L5 Gene in Nilaparvata lugens (Hemiptera: Delphacidae)

The ribosomal proteins play important roles in the growth and development of organisms. This study aimed to explore the function of NlRPL5 (GenBank KX379234), a ribosomal protein L5 gene, in the brown planthopper Nilaparvata lugens. The open reading frame of NlRPL5 was cloned from N. lugens based on a previous transcriptome analysis. The results revealed that the open reading frame of NlRPL5 is of 900 bp, encoding 299 amino acid residues. The reverse transcription quantitative PCR results suggested that the expression of NlRPL5 gene was stronger in gravid females, but was relatively low in nymphs, males, and newly emerged females. The expression level of NlRPL5 in the ovary was about twofolds of that in the head, thorax, or fat body. RNAi of dsNlRPL5 resulted in a significant reduction of mRNA levels, ∼50% decrease in comparison with the dsGFP control at day 6. Treatment of dsNlRPL5 significantly restricted the ovarian development, and decreased the number of eggs laid on the rice (Oryza sativa) plants. This study provided a new clue for further study on the function and regulation mechanism of NlRPL5 in N. lugens.
The acceptability of PEGASUS: an intervention to facilitate shared decision-making with women contemplating breast reconstruction

Good practice guidelines recommend that women who undergo mastectomy are offered reconstructive surgery. However, many who choose this option report a degree of decisional regret and dissatisfaction because their pre-surgical expectations were not met. This paper reports an acceptability study of a new intervention (PEGASUS) that aims to support shared decision-making by eliciting women’s pre-surgical expectations and setting patient-centred goals. Eighteen women contemplating breast reconstruction completed the PEGASUS intervention. Semi-structured interviews were conducted with 12 women and 3 health professionals to explore their experiences of using PEGASUS. Interview transcripts were subjected to a thematic analysis, and a content analysis was conducted on 79 goals that the 18 women identified. Feedback was extremely positive – women found that completing PEGASUS alongside a discussion with a specially trained health professional helped them prepare for the surgical consultation and increased their trust in their surgeon. Staff reported that PEGASUS facilitated patient-centred discussions and informed the decisions made about potential surgery. This preliminary study suggests that this novel intervention is acceptable to patients and health professionals alike. Further work is needed to evaluate its efficacy and then its effectiveness with a larger sample of women, and its potential use with other patient groups.
Measuring residual stresses in metallic components manufactured with fibre Bragg gratings embedded by selective laser melting

Metal clad single mode optical fibres containing Fibre Bragg Gratings are embedded in stainless steel components using bespoke laser based Selective Laser Melting technology (SLM). Significant residual stresses can be created in SLM manufactured components through the strong thermal gradients during the build process. We demonstrate the ability to monitor these internal stresses through embedded optical fibres with FBGs on a layer to layer basis, confirming estimates from models for residual stresses in additive manufactured components.
Supervised Collective Classification for Crowdsourcing

Crowdsourcing utilizes the wisdom of crowds for collective classification via information (e.g., labels of an item) provided by labelers. Current crowdsourcing algorithms are mainly unsupervised methods that are unaware of the quality of crowdsourced data. In this paper, we propose a supervised collective classification algorithm that aims to identify reliable labelers from the training data (e.g., items with known labels). The reliability (i.e., weighting factor) of each labeler is determined via a saddle point algorithm. The results on several crowdsourced data show that supervised methods can achieve better classification accuracy than unsupervised methods, and our proposed method outperforms other algorithms.
bioSync: Synchronous Kinesthetic Experience among People

This paper presents synchronous kinesthetic interaction among people. The users are able to perceive muscle activity bi-directionally, such as muscle contraction or rigidity of joints, through somatosensory channels in a realistic manner. We have developed a wearable haptic I/O device, named bioSync, that equips a developed electrode system for enabling the same electrodes to perform biosignal measurement and stimulation. We conducted a pilot study to evaluate the optimal forms of a feeding spoon for people with neuromuscular disorders by reproducing muscle tremors in healthy people. Potential scenarios for achieving interactive rehabilitations and sports training are also described. It is essential for both the trainers and the learners to perceive not only the physical bodily motions but also the muscle activity.
A Trichotomy in the Data Complexity of Certain Query Answering for Conjunctive Queries

A relational database is said to be uncertain if primary key constraints can possibly be violated. A repair (or possible world) of an uncertain database is obtained by selecting a maximal number of tuples without ever selecting two distinct tuples with the same primary key value. For any Boolean query q, CERTAINTY(q) is the problem that takes an uncertain database db on input, and asks whether q is true in every repair of db. The complexity of this problem has been particularly studied for q ranging over the class of self-join-free Boolean conjunctive queries. A research challenge is to determine, given q, whether CERTAINTY(q) belongs to complexity classes FO, P, or coNP-complete. In this paper, we combine existing techniques for studying the above complexity classification task. We show that for any self-join-free Boolean conjunctive query q, it can be decided whether or not CERTAINTY(q) is in FO. Further, for any self-join-free Boolean conjunctive query q, CERTAINTY(q) is either in P or coNP-complete, and the complexity dichotomy is effective. This settles a research question that has been open for ten years, since [9].
Basis Function Discovery Using Spectral Clustering and Bisimulation Metrics

We study the problem of automatically generating features for function approximation in reinforcement learning. We build on the work of Mahadevan and his colleagues, who pioneered the use of spectral clustering methods for basis function construction. Their methods work on top of a graph that captures state adjacency. Instead, we use bisimulation metrics in order to provide state distances for spectral clustering. The advantage of these metrics is that they incorporate reward information in a natural way, in addition to the state transition information. We provide theoretical bounds on the quality of the obtained approximation, which justify the importance of incorporating reward information. We also demonstrate empirically that the approximation quality improves when bisimulation metrics are used instead of the state adjacency graph in the basis function construction process.
A Randomized Gossip-based Algorithm for Classification on Peer-to-Peer Networks

Peer-to-Peer (P2P) networks are distributed systems in which nodes of equal roles and capabilities exchange information and services directly with one another. In recent years, they have become a popular way to share large amounts of data. Such architectures, however, complicate the process of knowledge discovery and data mining since algorithms must deal with distributed (and often) dynamic sources of data and computing. In this paper, we present a distributed algorithm for learning linear classifiers in P2P networks. The problem is posed as a linear program such that each peer has its own constraints, but needs to solve a global objective function. A randomized-gossip based approximate algorithm is presented which reduces communication cost in the network significantly while ensuring convergence of the algorithm.
Cascading extinctions and community collapse in model food webs

Species loss in ecosystems can lead to secondary extinctions as a result of consumer–resource relationships and other species interactions. We compare levels of secondary extinctions in communities generated by four structural food-web models and a fifth null model in response to sequential primary species removals. We focus on various aspects of food-web structural integrity including robustness, community collapse and threshold periods, and how these features relate to assumptions underlying different models, different species loss sequences and simple measures of diversity and complexity. Hierarchical feeding, a fundamental characteristic of food-web structure, appears to impose a cost in terms of robustness and other aspects of structural integrity. However, exponential-type link distributions, also characteristic of more realistic models, generally confer greater structural robustness than the less skewed link distributions of less realistic models. In most cases for the more realistic models, increased robustness and decreased levels of web collapse are associated with increased diversity, measured as species richness S, and increased complexity, measured as connectance C. These and other results, including a surprising sensitivity of more realistic model food webs to loss of species with few links to other species, are compared with prior work based on empirical food-web data.