Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones

Comparative transcriptomics between species can provide valuable understanding of plant-pathogen interactions. Here, we focus on wild Solanum species and potato clones with varying degree of resistance against Phytophthora infestans, which causes the devastating late blight disease in potato. The transcriptomes of three wild Solanum species native to Southern Sweden, Solanum dulcamara, Solanum nigrum, and Solanum physalifolium were compared to three potato clones, Desiree (cv.), SW93-1015 and Sarpo Mira. Desiree and S. physalifolium are susceptible to P. infestans whereas the other four have different degrees of resistance. By building transcript families based on de novo assembled RNA-seq across species and clones and correlating these to resistance phenotypes, we created a novel workflow to identify families with expanded or depleted number of transcripts in relation to the P. infestans resistance level. Analysis was facilitated by inferring functional annotations based on the family structure and semantic clustering. More transcript families were expanded in the resistant clones and species and the enriched functions of these were associated to expected gene ontology (GO) terms for resistance mechanisms such as hypersensitive response, host programmed cell death and endopeptidase activity. However, a number of unexpected functions and transcripts were also identified, for example transmembrane transport and protein acylation expanded in the susceptible group and a cluster of Zinc knuckle family proteins expanded in the resistant group. Over 400 expressed putative resistance (R-)genes were identified and resistant clones Sarpo Mira and SW93-1015 had ca 25% more expressed putative R-genes than susceptible cultivar Desiree. However, no differences in numbers of susceptibility (S-)gene homologs were seen between species and clones. In addition, we identified P. infestans transcripts including effectors in the early stages of P. infestans-Solanum interactions.
GJA1 mutations, variants, and connexin 43 dysfunction as it relates to the oculodentodigital dysplasia phenotype

The predominantly autosomal dominant disorder, oculodentodigital dysplasia (ODDD) has high penetrance with intra‐ and interfamilial phenotypic variability. Abnormalities observed in ODDD affect the eye, dentition, and digits of the hands and feet. Patients present with a characteristic facial appearance, narrow nose, and hypoplastic alae nasi. Neurological problems, including dysarthria, neurogenic bladder disturbances, spastic paraparesis, ataxia, anterior tibial muscle weakness, and seizures, are known to occur as well as conductive hearing loss, cardiac defects, and anomalies of the skin, hair, and nails. In 2003, our analysis of 17 ODDD families revealed that each had a different mutation within the human gap junction alpha 1 (GJA1) gene which encodes the protein connexin 43 (Cx43). Since then at least 17 publications have identified an additional 26 GJA1 mutations and in this study, we present 28 new cases with 18 novel GJA1 mutations. We include tables summarizing the 62 known GJA1 nucleotide changes leading to Cx43 protein alterations and the phenotypic information available on 177 affected individuals from 54 genotyped families. Mutations resulting in ODDD occur in each of the nine domains of the Cx43 protein, and we review our functional experiments and those in the literature, examining the effects of 13 different Cx43 mutations upon gap junction activity. Hum Mutat 0, 1–10, 2009. © 2009 Wiley‐Liss, Inc.
ON THE ZEROS OF COSINE POLYNOMIALS : SOLUTION TO AN OLD PROBLEM OF LITTLEWOOD

Littlewood in his 1968 monograph “Some Problems in Real and Complex Analysis” [10, problem 22] poses the following research problem, which appears to still be open: Problem. “If the nj are integral and all different, what is the lower bound on the number of real zeros of PN j=1 cos(njθ)? Possibly N −1, or not much less. ” No progress appears to have been made on this in the last half century. We show that this is false. Theorem. There exists a cosine polynomial PN j=1 cos(njθ) with the nj integral and all different so that the number of its real zeros in the period is O “ N(log N) ” . 1. Littlewood’s 22nd Problem Problem. “If the nj are integral and all different, what is the lower bound on the number of real zeros of ∑N j=1 cos(njθ)? Possibly N − 1, or not much less. ” Here “real zeros” means “zeros in a period”. Denote the number of zeros of a trigonometric polynomial T in the period [−π, π) by N (T ). Note that if T is a real trigonometric cosine polynomial of degree n, then it is of the form T (t) = exp(−int)P (exp(it)), t ∈ R, where P is a reciprocal algebraic polynomial of degree 2n, and if T has only real zeros, then P has all its zeros on the unit circle. So in terms or reciprocal algebraic polynomials one is looking for a reciprocal algebraic polynomial with coefficients in {0, 1}, with 2N terms, and with N − 1 or fewer zeros. Even achieving N − 1 is fairly hard. An exhaustive search up to degree 2N = 32 yields only 1
The Lack of Predictors for Rapid Progression in Prostate Cancer Patients Receiving Sipuleucel-T

Sipuleucel-T is an immunotherapy indicated for the treatment of metastatic prostate cancer. It offers a new mechanism to treat prostate cancer without the side effects of hormone therapies and chemotherapies. In previous studies sipuleucel-T did not delay disease progression, but demonstrated an overall survival benefit compared to placebo. While clinical trials have evaluated the effects of sipuleucel-T on overall survival and progression, more studies are needed to evaluate its effectiveness and role in the management of prostate cancer. The objective of this study is to identify the incidence and possible predictors for disease progression in patients receiving sipuleucel-T. A retrospective review of patients who received sipuleucel-T between 1 September 2010 and 11 October 2011 was conducted (n = 36). Patients who changed therapy or died within 120 days were classified as experiencing rapid progression. Potential predictors of rapid progression were examined using logistic regression. Seven patients met criteria for rapid progression. Progression occurred in 72.2% of all patients. The median days to progression was 158. No significant predictors of rapid progression were identified. Currently no predictors have been found to be associated with rapid progression in prostate cancer patients on sipuleucel-T.
The 37‐kDa/67‐kDa laminin receptor acts as the cell‐surface receptor for the cellular prion protein

Recently, we identified the 37‐kDa laminin receptor precursor (LRP) as an interactor for the prion protein (PrP). Here, we show the presence of the 37‐kDa LRP and its mature 67‐kDa form termed high‐affinity laminin receptor (LR) in plasma membrane fractions of N2a cells, whereas only the 37‐kDa LRP was detected in baby hamster kidney (BHK) cells. PrP co‐localizes with LRP/LR on the surface of N2a cells and Semliki Forest virus (SFV) RNA transfected BHK cells. Cell‐binding assays reveal the LRP/LR‐dependent binding of cellular PrP by neuronal and non‐neuronal cells. Hyperexpression of LRP on the surface of BHK cells results in the binding of exogenous PrP. Cell binding is similar in PrP+/+ and PrP0/0 primary neurons, demonstrating that PrP does not act as a co‐receptor of LRP/LR. LRP/LR‐dependent internalization of PrP is blocked at 4°C. Secretion of an LRP mutant lacking the transmembrane domain (aa 86–101) from BHK cells abolishes PrP binding and internalization. Our results show that LRP/LR acts as the receptor for cellular PrP on the surface of mammalian cells.
Optical quality of the eye in subjects with normal and excellent visual acuity.

PURPOSE To study the relationship between visual acuity (VA) and the eye's optical quality in subjects with normal and excellent spatial vision. VA ranged from decimal values of 1.0 (20/20) to 2.0 (20/10) when defocus and astigmatism were carefully corrected. METHODS In 60 eyes of young subjects, visual and optical performance with the natural pupil were measured. A forced-choice procedure was used to measure tumbling-E high-contrast VA (HCVA) and low-contrast VA (LCVA). Wavefront aberration (WA) was measured using a Hartmann-Shack sensor. The associated point-spread function (PSF) and modulation transfer function (MTF) were also estimated. High-order aberrations (HOA) and several image quality parameters were represented as a function of VA. Subjects were classified into three groups according to their VA, and average optical parameters were calculated. RESULTS Coma and trefoil vary between 0 and 0.5 mum, and spherical aberration ranges from -0.40 mum to +0.45 mum, with an average value of approximately zero. LCVA is not correlated with any of the aberration terms. Coma and spherical aberration are not correlated with HCVA. However, eyes with trefoil equal to or higher than 0.25 mum have an HCVA less than 1.5. The average optical quality in eyes with HCVA greater than 1.4 is slightly better than in eyes with normal VA. However, some eyes had relatively poor image quality and excellent VA. CONCLUSIONS No significant correlations were found between VA measurements and the optical quality of the eye in young subjects with normal or excellent spatial vision. Some subjects with normal degrees of aberrations attained excellent VA.
How to Transfer? Zero-Shot Object Recognition via Hierarchical Transfer of Semantic Attributes

Attribute based knowledge transfer has proven very successful in visual object analysis and learning previously unseen classes. However, the common approach learns and transfers attributes without taking into consideration the embedded structure between the categories in the source set. Such information provides important cues on the intraattribute variations. We propose to capture these variations in a hierarchical model that expands the knowledge source with additional abstraction levels of attributes. We also provide a novel transfer approach that can choose the appropriate attributes to be shared with an unseen class. We evaluate our approach on three public datasets: a Pascal, Animals with Attributes and CUB-200-2011 Birds. The experiments demonstrate the effectiveness of our model with significant improvement over state-of-the-art.
Visual search with emotional faces

It has been proposed that threatening stimuli can automatically attract attention and are detected faster; conferring evolutionary advantages for an organism’s well-being and survival (Becker, Horstmann, & Remington, 2011). In line with the threat hypothesis, studies demonstrated that angry faces are detected faster among happy faces (Belopolsky, Devue & Theeuwes, 2011; Lipp, Price, & Tellegan, 2009). However, other studies demonstrated the opposite (Becker et al., 2011; Calvo & Nummenmaa, 2008). Hence, some researchers proposed that instead of emotional expressions, perceptual saliency of faces determines detection speed as visible teeth may render faces salient. A potential explanation of previous discrepant results is that the visibility of teeth was not controlled in previous studies, as studies reporting a happy-face advantage often pitted open-mouth happy faces against closed-mouth angry faces and vice versa. The current study compared the effects of teeth visibility and emotional expression in a visual search task where participants (N=24) searched for an emotional target face among neutral distracters; and a second task (N=24) where participants conducted the same search with the addition of an emotional distracter. To explore effects of other perceptual factors on search performance, participants rated emotional faces for (1) their similarity to same emotion faces; (2) their dissimilarity to the neutral distracter faces. In line with the perceptual saliency hypothesis, faces that were detected faster were rated as more dissimilar from non-targets. Participants’ eye movements were used to measure the time-course of attention shifts to the target and distracters. The results showed that the visibility of teeth determined attention shifts and eye movements more strongly than emotional expression: More first eye movements were made to open-mouth faces than closed-mouth faces. In line with the perceptual account, results showed that visible teeth can attract attention independent of the emotion and threat potential of the faces.
EVALUATION OF SERUM FERRITIN AND SERUM IRON IN FREE-RANGING BLACK RHINOCEROS (DICEROS BICORNIS) AS A TOOL TO UNDERSTAND FACTORS AFFECTING IRON-OVERLOAD DISORDER

Abstract Iron overload disorder (IOD) is a significant health issue for captive black rhinoceros (Diceros bicornis). Measurement of serum ferritin with a validated rhinoceros ferritin ELISA has been used extensively to detect animals in U.S. zoos that are at risk of developing IOD. However, there is limited information on serum ferritin levels in free-ranging black rhinoceros using this same assay. Serum ferritin, iron, and gamma-glutamyl transpeptidase (GGT) were determined in 194 black rhinoceros from southern Africa. Mean ferritin in free-ranging black rhinoceros (290.54 ±247.4 ng/ml) was significantly higher than in free-ranging white rhinoceros (64.0 ± 102.4 ng/ml) sampled in this study from Kruger National Park, South Africa. However, there were no significant differences between genders or age groups. Ferritin values varied with geographical location of the black rhinoceros, although this was not clinically significant. Serum iron values were also higher in black rhinoceros (40.4 ± 19.1 μmol/L) compared to white rhinoceros (29.7 ± 10.7 μmol/L). There was no association between ferritin and GGT. This study provides serum ferritin, iron, and GGT values from free-ranging black rhinoceros that can be used for as comparative target values for captive animals.
Base-Pairing Versatility Determines Wobble Sites in tRNA Anticodons of Vertebrate Mitogenomes

Background Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA) for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick base pairing between two nucleotides in RNA molecules) to recognize one or more synonymous codons. Different hypotheses have been proposed to explain the factors that determine the nucleotide composition of wobble sites in vertebrate mitochondrial tRNA anticodons. Until now, the two major postulates – the “codon-anticodon adaptation hypothesis” and the “wobble versatility hypothesis” – have not been formally tested in vertebrate mitochondria because both make the same predictions regarding the composition of anticodon wobble sites. The same is true for the more recent “wobble cost hypothesis”. Principal Findings In this study we have analyzed the occurrence of synonymous codons and tRNA anticodon wobble sites in 1553 complete vertebrate mitochondrial genomes, focusing on three fish species with mtDNA codon usage bias reversal (L-strand is GT-rich). These mitogenomes constitute an excellent opportunity to study the evolution of the wobble nucleotide composition of tRNA anticodons because due to the reversal the predictions for the anticodon wobble sites differ between the existing hypotheses. We observed that none of the wobble sites of tRNA anticodons in these unusual mitochondrial genomes coevolved to match the new overall codon usage bias, suggesting that nucleotides at the wobble sites of tRNA anticodons in vertebrate mitochondrial genomes are determined by wobble versatility. Conclusions/Significance Our results suggest that, at wobble sites of tRNA anticodons in vertebrate mitogenomes, selection favors the most versatile nucleotide in terms of wobble base-pairing stability and that wobble site composition is not influenced by codon usage. These results are in agreement with the “wobble versatility hypothesis”.
Impulse Control Disorders in Parkinson’s Disease: Crossroads between Neurology, Psychiatry and Neuroscience

Non-motor symptoms contribute significantly to Parkinson’s disease (PD) related disability. Impulse control disorders (ICDs) have been recently added to the behavioural spectrum of PD-related non-motor symptoms. Such behaviours are characterized by an inappropriate drive to conduct repetitive behaviours that are usually socially inadequate or result in harmful consequences. Parkinson disease impulse control disorders (PD-ICDs) have raised significant interest in the scientific and medical community, not only because of their incapacitating nature, but also because they may represent a valid model of ICDs beyond PD and a means to study the physiology of drive, impulse control and compulsive actions in the normal brain. In this review, we discuss some unresolved issues regarding PD-ICDs, including the association with psychiatric co-morbidities such as obsessive-compulsive disorder and with dopamine related side effects, such as hallucinations and dyskinesias; the relationship with executive cognitive dysfunction; and the neural underpinnings of ICDs in PD. We also discuss the contribution of neuroscience studies based on animal-models towards a mechanistic explanation of the development of PD-ICDs, specifically regarding corticostriatal control of goal directed and habitual actions.
A simple spectral algorithm for recovering planted partitions

Abstract In this paper, we consider the planted partition model, in which n = ks vertices of a random graph are partitioned into k “clusters,” each of size s. Edges between vertices in the same cluster and different clusters are included with constant probability p and q, respectively (where 0 ≤ q < p ≤ 1). We give an efficient algorithm that, with high probability, recovers the clusters as long as the cluster sizes are are least (√n). Informally, our algorithm constructs the projection operator onto the dominant k-dimensional eigenspace of the graph’s adjacency matrix and uses it to recover one cluster at a time. To our knowledge, our algorithm is the first purely spectral algorithm which runs in polynomial time and works even when s = Θ (√n), though there have been several non-spectral algorithms which accomplish this. Our algorithm is also among the simplest of these spectral algorithms, and its proof of correctness illustrates the usefulness of the Cauchy integral formula in this domain.
Model for End‐Stage Liver Disease score does not predict patient or graft survival in living donor liver transplant recipients

Although living donor liver transplantation (LDLT( is a successful procedure for most recipients, outcomes in patients who undergo transplantation as United Network for Organ Sharing status 2A are marginal. There are no published data on living donor liver transplant recipient outcomes relative to Model for End‐Stage Liver Disease (MELD( scores. Such information could be useful in living donor liver transplant recipient selection. We retrospectively analyzed all non‐fulminant hepatic failure, right hepatic lobe, adult‐to‐adult living donor liver transplant recipients at our center between August 1997 and March 2002. We calculated MELD scores at the time of LDLT and correlated scores with 1‐year patient and graft survival and hospital days during the 90‐day post‐LDLT period. There were 62 recipients with greater than 6 months of follow‐up: 38 men, 24 women; mean age, 47.9 years; 42 white, 1 black, 17 Hispanic, and 2 Asian patients. Twenty‐nine patients had hepatitis C virus infection; 4 patients, hepatitis C virus infection and alcoholic liver disease; 4 patients, alcoholic liver disease; 4 patients, cryptogenic cirrhosis; 13 patients, primary sclerosing cholangitis; 5 patients, autoimmune hepatitis; and 3 patients, primary biliary cirrhosis. Mean and median MELD scores were 15.2 and 13, respectively (range, 6 to 40(. One‐year patient and graft survival were 59 of 62 patients (95%( and 52 of 62 patients (84%(, respectively. There was no statistically significant difference between median MELD scores of dead versus living patients (15 v 13; P = . 15( or patients who underwent retransplantation versus those who did not (16.5 v 13; P = . 30(. Mean and median hospital days in the 90‐day post‐LDLT period were 23.7 and 16.0 days, respectively. Living donor liver transplant recipients with a MELD score of 18 or greater had significantly more hospital days compared with recipients with a MELD score less than 18 (35.2 v 19.8 days; P = . 01(. In conclusion, MELD scores did not predict post‐LDLT patient or graft survival at 1 year. However, higher MELD scores (≥18( were associated with more hospital days during the 3‐month post‐LDLT period. (Liver Transpl 2003;9:737‐740. (
Resource containers: a new facility for resource management in server systems

General-purpose operating systems provide inadequate support for resource management in large-scale servers. Applications lack sufficient control over scheduling and management of machine resources, which makes it difficult to enforce priority policies, and to provide robust and controlled service. There is a fundamental mismatch between the original design assumptions underlying the resource management mechanisms of current general-purpose operating systems, and the behavior of modern server applications. In particular, the operating system's notions of protection domain and resource principal coincide in the process abstraction. This coincidence prevents a process that manages large numbers of network connections, for example, from properly allocating system resources among those connections. We propose and evaluate a new operating system abstraction called a resource container, which separates the notion of a protection domain from that of a resource principal. Resource containers enable fine-grained resource management in server systems and allow the development of robust servers, with simple and firm control over priority policies.
A Bayesian Data Augmentation Approach for Learning Deep Models

Data augmentation is an essential part of the training process applied to deep learning models. The motivation is that a robust training process for deep learning models depends on large annotated datasets, which are expensive to be acquired, stored and processed. Therefore a reasonable alternative is to be able to automatically generate new annotated training samples using a process known as data augmentation. The dominant data augmentation approach in the field assumes that new training samples can be obtained via random geometric or appearance transformations applied to annotated training samples, but this is a strong assumption because it is unclear if this is a reliable generative model for producing new training samples. In this paper, we provide a novel Bayesian formulation to data augmentation, where new annotated training points are treated as missing variables and generated based on the distribution learned from the training set. For learning, we introduce a theoretically sound algorithm --- generalised Monte Carlo expectation maximisation, and demonstrate one possible implementation via an extension of the Generative Adversarial Network (GAN). Classification results on MNIST, CIFAR-10 and CIFAR-100 show the better performance of our proposed method compared to the current dominant data augmentation approach mentioned above --- the results also show that our approach produces better classification results than similar GAN models.