Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial DNA (mtDNA) in brain samples from patients with major psychiatric disorders: Gene expression profiles, MtDNA content and presence of the MtDNA common deletion

Several lines of evidence support a mitochondrial dysfunction in major psychiatric disorders. The objective of this study was to determine whether mitochondrial DNA (mtDNA) expression or content are implicated in the mitochondrial dysfunction observed in schizophrenia (SCH), bipolar disorder (BD), and major depressive disorder (MDD). MtDNA gene expression and mtDNA content (including the MT‐ND4 deletion) were measured by RT‐qPCR and qPCR, respectively. Post‐mortem brain tissue from 60 subjects, divided evenly into four diagnostic groups (SCH, BD, MDD, and control (C)), was analyzed. MT‐ND1 gene expression was significantly increased in the BD group compared with the C group. MDD and SCH patients showed a similar pattern of mtDNA expression, which was different from that in BD patients. Similarly, a larger number of MDD and SCH patients tended to have the MT‐ND4 gene deleted compared with BD and C subjects. However, no other significant differences were observed in mtDNA gene expression and mtDNA content. Notably, high variability was observed in the mtDNA gene expression and content in each diagnostic group. Previous studies and the present work provide evidence for a role of mtDNA in SCH, BD and MDD. However, further studies with larger patient and control groups as well as by analyzing distinct brain regions are needed to elucidate the role of mtDNA in major psychiatric disorders. © 2013 Wiley Periodicals, Inc.
The Classification of Hyperspectral Images Based on Band-Grouping and Convolutional Neural Network

For the classification of hyperspectral images, a classification algorithm based on band grouping and three-dimensional convolutional neural network(3D-CNN-BG) is proposed. The algorithm uses the correlation matrix of hyperspectral images to determine the similarity of bands, and the high similarity bands are grouped together. Then, every bands group is extracted spatial-spectral feature using 3D convolutional neural network. Finally, the high-level feature of every 3D-CNN is stacked together trained by the classifier. With band regroup, the feature in the similar group can be extracted fully by the 3D-CNN, which is good for classification. The experiments showed that compared with other hyperspectral images classification algorithms based on CNN, the proposed algorithm converges more faster, has less training parameters, and acquires higher classification accuracy. After training 100 times, the overall classification accuracy on the indian pines data set can reach 97.42%, increased by approximately 2% ~ 5%, which shows the strong practicability of proposed algorithm in hyperspectral application
Biology of taste buds and the clinical problem of taste loss

Taste buds are the anatomical structures that mediate the sense of taste. They comprise taste cells and nerve fibers within specialized epithelial structures. Taste cells are traditionally described by histologic methods as basal, dark, intermediate, and light cells, with the nerve fibers surrounding and infiltrating the taste buds. By means of immunohistochemical methods, taste cells and gustatory nerve fibers can be classified in functional groups based on the expression of various cell adhesion molecules and other proteins. When taste buds become damaged, the loss of the ability to taste results. This loss is not uncommon and can impact health and quality of life. Patients who receive radiation therapy for head and neck cancer often experience taste loss, which leads to compromised nutritional intake and a worse outcome than patients who do not experience taste loss. The mode of radiation damage to taste cells and nerve fibers has been investigated using cell adhesion molecules, synaptic vesicle proteins, and other cell markers. The light and intermediate cells are preferentially affected by ionizing radiation, whereas the nerve fibers remain structurally intact. Experimental studies of radiation‐induced taste loss are performed via a unique animal/human model. Anat. Rec. (New Anat.) 253:70–78, 1998. © 1998 Wiley‐Liss, Inc.
Amyotrophic Lateral Sclerosis from Bench to Bedside

Amyotrophic lateral sclerosis (ALS) is a progressive disease for which there are currently no significant treatments to alter the fatal outcome. The cause of the disease is still elusive, except in familial cases where significant advances have been made in identifying new genetic causes. ALS is a relatively rare disease affecting approximately 1 in 100,000 people equally across geographic and ethnic distributions. It is a difficult disease to diagnose, and there are many mimics of ALS. Overlap with dementia may provide new clues to the etiology and treatment. There have been many advances in symptomatic treatments and improvements in the quality of life for ALS patients due to technological advancements.
Velocity estimation from images sequence and application to super-resolution

We present a method for approximating optical flow (velocity field) by a scaled piece-wise regular vector field. The method can be formulated in a variational manner that has a strong analogy to the Mumford and Shah (1985) functional for segmenting gray level image and in particular to the region merging minimization procedure described by Morel and Soluminini (1995). The proposed functional balances a complexity term (which can be the usual sum of the boundary length) to the "ability" of pixels to move together (that is with the same model of velocity regardless of what it is). A key point that allows the method to overcome, to some extent, the non-uniqueness of the optical flow is that the segmentation is performed without any attribution of velocities to pixels or regions. Finally, we show that the obtained velocity field is, in some cases, accurate enough to perform a "Frame-Fusion" process. We show some applications of this "super-resolution" for law enforcement.
Identifying Age Based Maturation in the ERP Response to Faces in Children With Autism: Implications for Developing Biomarkers for Use in Clinical Trials

Recent proposals have suggested the potential for neural biomarkers to improve clinical trial processes in neurodevelopmental conditions; however, few efforts have identified whether chronological age-based adjustments will be necessary (as used in standardized behavioral assessments). Event-related potentials (ERPs) demonstrate early differences in the processing of faces vs. objects in the visual processing system by 4 years of age and age-based improvement (decreases in latency) through adolescence. Additionally, face processing has been proposed to be related to social skills as well as autistic social-communication traits. While previous reports suggest delayed latency in individuals with autism spectrum disorder (ASD), extensive individual and age based heterogeneity exists. In this report, we utilize a sample of 252 children with ASD and 118 children with typical development (TD), to assess the N170 and P100 ERP component latencies (N170L and P100L, respectively), to upright faces, the face specificity effect (difference between face and object processing), and the inversion effect (difference between face upright and inverted processing) in relation to age. First, linear mixed models (LMMs) were fitted with fixed effect of age at testing and random effect of participant, using all available data points to characterize general age-based development in the TD and ASD groups. Second, LMM models using only the TD group were used to calculate age-based residuals in both groups. The purpose of residualization was to assess how much variation in ASD participants could be accounted for by chronological age-related changes. Our data demonstrate that the N170L and P100L responses to upright faces appeared to follow a roughly linear relationship with age. In the ASD group, the distribution of the age-adjusted residual values suggest that ASD participants were more likely to demonstrate slower latencies than would be expected for a TD child of the same age, similar to what has been identified using unadjusted values. Lastly, using age-adjusted values for stratification, we found that children who demonstrated slowed age-adjusted N170L had lower verbal and non-verbal IQ and worse face memory. These data suggest that age must be considered in assessing the N170L and P100L response to upright faces as well, and these adjusted values may be used to stratify children within the autism spectrum.
The state space framework for blind dynamic signal extraction and recovery

The paper describes a framework in the form of an optimization of a performance index subject to the constraints of a dynamic network, represented in the state space. The performance index is a measure of statistical dependence among the outputs of the network, namely, the relative entropy also known as the Kullback-Leibler divergence. The network is represented as (either discrete or continuous time) state space dynamics. Update laws are derived in the general cases. Moreover, in the discrete-time case, they are shown to specialize in the FIR and IIR network representations.
Dyspepsia in the community is linked to smoking and aspirin use but not to Helicobacter pylori infection.

BACKGROUND The relationship between Helicobacter pylori infection and symptoms remains controversial. We aimed to determine if an association exists between unexplained dyspepsia (pain or discomfort centered in the upper part of the abdomen) and H pylori. METHODS A validated questionnaire was completed by 592 healthy blood donors. Helicobacter pylori serologic values (via enzyme-linked immunosorbent assay), blood group status, and Rh status were measured; 4.9% of subjects who had a history of peptic ulcer disease were excluded from the analyses. RESULTS The prevalence of dyspepsia and no ulcer history was 11% (95% confidence interval [CI], 8.6%-13.8%); 15.4% of subjects with dyspepsia had H pylori while 14.6% of subjects without dyspepsia were infected (P=.90). The mean dyspepsia impact scores (combining frequency and severity) in those with and without H pylori were 4.7 and 5.4, respectively (P=.20). The median H pylori optical density values in dyspepsia vs no dyspepsia were not significantly different (P=.30). Independent risk factors for dyspepsia were the use of aspirin (odds ratio [OR], 2.2; 95% CI, 1.3-3.7) and smoking (OR, 2.1; 95% CI, 1.3-3.6) but not age, sex, marital status, educational level, income, or the use of alcohol, coffee, or nonsteroidal anti-inflammatory drugs. Independent risk factors for H pylori were increasing age (OR, 1.8 per decade; 95% CI, 1.5-2.3), male sex (OR, 2.1; 95% CI, 1.3-3.4), and net family income (OR, 1.8; 95% CI, 1.2-3.3). CONCLUSION Dyspepsia in the community is linked to smoking and aspirin use, but not to H pylori infection.
Pharmacologic Treatment of Patent Ductus Arteriosus in the Preterm Infant

P atent ductus arteriosus (PDA) is one of the most common clinical findings in preterm infants. Patent ductus arteriosus occurs when the ductus arteriosus fails to close following birth and is most often found in the setting of prematurity, affecting approximately 50% of all preterm infants. Patent ductus arteriosus with significant left-to-right shunts have been associated with increased morbidity in preterm infants for more than 50 years. Hemodynamically significant PDAs cause decreased renal blood flow, intestinal ischemia, and decreased cerebral artery blood flow. In addition, PDAs produce high pulmonary blood flow, often in the setting of surfactant deficiency and increased capillary permeability, which results in pulmonary edema and increased ventilation requirements. In extremely preterm infants, these alterations in vital organ blood flow may increase the risk of necrotizing enterocolitis, intraventricular hemorrhage, periventricular leukomalacia, and chronic lung disease (CLD). These morbidities are common complications of preterm birth and a causative link to PDA has not been proven. Care of the preterm infant with PDA in the neonatal intensive care unit is an ongoing challenge. Little consensus regarding treatment of PDA currently exists. Treatment requires careful consideration of the risks and benefits of available therapies, namely, surgical ligation and pharmacological interventions. While surgery typically results in reliable closure of the PDA, it is also associated with both shortand long-term surgical complications including infection and neurodevelopmental impairment. For this reason, surgical ligation of the PDA is usually considered only after medical treatment, which is focused primarily on a pharmacological approach to closing the PDA. Here, I briefly review both
Effect of anti-IgE therapy in patients with peanut allergy.

BACKGROUND Peanut-induced anaphylaxis is an IgE-mediated condition that is estimated to affect 1.5 million people and cause 50 to 100 deaths per year in the United States. TNX-901 is a humanized IgG1 monoclonal antibody against IgE that recognizes and masks an epitope in the CH3 region of IgE responsible for binding to the high-affinity Fc(epsilon) receptor on mast cells and basophils. METHODS We conducted a double-blind, randomized, dose-ranging trial in 84 patients with a history of immediate hypersensitivity to peanut. Hypersensitivity was confirmed and the threshold dose of encapsulated peanut flour established by a double-blind, placebo-controlled oral food challenge at screening. Patients were randomly assigned in a 3:1 ratio to receive either TNX-901 (150, 300, or 450 mg) or placebo subcutaneously every four weeks for four doses. The patients underwent a final oral food challenge within two to four weeks after the fourth dose. RESULTS From a mean base-line threshold of sensitivity of 178 to 436 mg of peanut flour in the various groups, the mean increases in the oral-food-challenge threshold were 710 mg in the placebo group, 913 mg in the group given 150 mg of TNX-901, 1650 mg in the group given 300 mg of TNX-901, and 2627 mg in the group given 450 mg of TNX-901 (P<0.001 for the comparison of the 450-mg dose with placebo, and P for trend with increasing dose <0.001). TNX-901 was well tolerated. CONCLUSIONS A 450-mg dose of TNX-901 significantly and substantially increased the threshold of sensitivity to peanut on oral food challenge from a level equal to approximately half a peanut (178 mg) to one equal to almost nine peanuts (2805 mg), an effect that should translate into protection against most unintended ingestions of peanuts.
Big data analytics concepts and management techniques

Emergence of big data sources at a rapid rate extends the necessity of old data organization due to the large volume, velocity, variety, value, and veracity of this data. Performing timely analysis on huge datasets is the central promise of big data analytics. The frameworks used to compose analytics jobs into a Directed Acyclic Graphs of small tasks, and then aggregate the intermediate results from the tasks to obtain the final result, does so with the help of a scheduler and a reliable storage layer that distributes the datasets on different machines. This paper presents the above two aspects, scheduling and storage, describe their key principles, and how these principles are realized in widely-deployed systems. The aim of this research project is to design a novel memory management for in-memory databases. Special designed hardware architectures can support the memory management of the host processor. This paper also explores how special designed hardware architectures can upkeep and fast-track data attainment, data straining and data investigation.
Ecological hazard assessment of major veterinary benzimidazoles: Acute and chronic toxicities to aquatic microbes and invertebrates

Aquatic toxicities of six benzimidazole‐based anthelmintics—namely, albendazole, thiabendazole, flubendazole, febantel, fenbendazole, and oxfendazole—were evaluated with a marine bacterium, Vibrio fischeri, and a freshwater invertebrate, Daphnia magna. Delayed and chronic toxicity tests using D. magna also were conducted for benzimidazoles with high acute toxicity. Vibrio fischeri was greater than 10‐fold less sensitive to most of the benzimidazoles tested compared to daphnids. For D. magna, the most acutely toxic anthelmintic compound tested was fenbendazole (48‐h median effective concentration [EC50s], 16.5 μg/L), followed by flubendazole (48‐h EC50, 66.5 μg/L), albendazole (48‐h EC50, 67.9 μg/L), febantel (48‐h EC50, 216.5 μg/L), thiabendazole (48‐h EC50, 843.6 μg/L), and oxfendazole (48‐h EC50, 1,168.4 μg/L). The lipophilicity parameter, log Kow, explained the observed acute D. magna toxicity of the individual benzimidazoles (r = −0.91, p < 0.01). Delayed expression of toxicity observed for 21 d after 96‐h exposure to fenbendazole and flubendazole was not notable, which might result from the relatively high elimination constants for the chemicals. With chronic exposure to fenbendazole, D. magna survival, reproduction, and growth were significantly impacted at 1.25 to 4.1 μg/L (p < 0.05). Hazard quotients estimated for fenbendazole, albendazole, flubendazole, and febantel were 2,770, 9.7, 4, and 1.2, respectively, suggesting a need for further investigation and a potential for environmental concerns, particularly with fenbendazole.
Reliability and validity of goniometric iPhone applications for the assessment of active shoulder external rotation

ABSTRACT Purpose/hypothesis: The purpose of this study was to determine the reliability and validity of two smartphone applications: (1) GetMyROM – inclinometery-based and (2) DrGoniometry – photo-based in the measurement of active shoulder external rotation (ER) as compared to standard goniometry (SG). Participants: Ninety-four Texas Woman's University Doctor of Physical Therapy students from the School of Physical Therapy – Houston campus, were recruited to participate in this study. Materials/methods: Two iPhone applications were compared to SG using both novice and experienced raters. Active shoulder ER range of motion was measured over two time periods in random order by blinded novice and experienced raters. Results: Intra-rater reliability using novice raters for the two applications ranged from an intraclass correlation coefficient (ICC) of 0.79 to 0.81 with SG at 0.82. Inter-rater reliability (novice/expert) for the two applications ranged from an ICC of 0.92 to 0.94 with SG at 0.91. Concurrent validity (when compared to SG) ranged from 0.93 to 0.94. There were no significant differences between the novice and experienced raters. Conclusion: Both applications were found to be reliable and comparable to SG. A photo-based application potentially offers a superior method of measurement as visualizing the landmarks may be simplified in this format and it provides a record of measurement. Clinical relevance: Further study using patient populations may find the two studied applications are useful as an adjunct for clinical practice.
Incipient speciation through niche expansion: an example from the Arctic charr in a subarctic lake

Two reproductive isolated morphs of Arctic charr (Salvelinus alpinus), termed profundal and littoral charr according to their different spawning habitats, co-occur in the postglacial lake Fjellfrøsvatn in North Norway. All profundal charr live in deep water their entire life and have a maximum size of 14 cm, while the littoral charr grow to 40 cm. Some small and young littoral charr move to the profundal zone in an ontogenetic habitat shift in the ice-free season and the rest of the population remains in epilimnic waters. The two morphs had different diet niches in the profundal zone: the profundal charr ate typical soft-bottom prey (chironomid larvae, pea mussels and benthic copepods), while the young littoral charr mainly consumed crustacean zooplankton. In four other lakes without a profundal morph (i.e. monomorphic populations), young charr also performed ontogenetic habitat shifts to the profundal zone and fed on zooplankton. The profundal morph of Fjellfrøsvatn therefore utilize a food resource niche that neither the littoral morph nor comparable monomorphic populations exploit. This suggests that intraspecific resource competition has driven incipient ecological speciation of the profundal charr of Fjellfrøsvatn. The exploitation of the soft-bottom resources by the profundal charr supports earlier experimental findings that the profundal morph is genetically different in trophic behaviour and morphology. The sympatric ecological divergence within the profundal habitat is possible because unexploited food resources (soft-bottom profundal prey) are available. Apparently, this represents a case of incipient segregation by expansion to new resource types (niche invasion), and not by subdivision of one broad ancestral niche.
Dynamic HIF1A Regulation During Human Placental Development1

Abstract The human placenta is a unique organ in terms of oxygenation as it undergoes a transition from a low to a more oxygenated environment. This physiological switch in oxygen tension is a prerequisite for proper placental development and involves the hypoxia inducible factor (HIF). HIF is stable and initiates gene transcription under hypoxia, whereas in normoxia, interaction with the von Hippel-Lindau tumor suppressor protein (VHL) leads to rapid degradation of the HIF1A subunit. The degradation requires formation of a multiprotein complex (VHLCBC) and hydroxylation of HIF1A proline residues via members of the egg-laying-defective nine (EGLN) family. Herein, we have investigated the regulatory mechanisms of HIF1A expression during human placental development. Expression of HIF1A and VHL was high at 7–9 wk of gestation, when oxygen tension is low, and decreased when placental oxygen tension increases (10–12 wk of gestation). During early placentation, HIF1A localized in cytotrophoblasts, while VHL was present in syncytiotrophoblasts. At 10–12 wk, VHL appeared in cytotrophoblast cells, which coincided with the disappearance of HIF1A. At the same time the association of VHL and Cullin 2 as well as ubiquitination of HIF1A was maximal. EGLN1, EGLN2, and EGLN3 were also temporally expressed in an oxygen-dependent fashion, with greatest mRNA expression at 10–12 wk of gestation. Inhibition of EGLN activity increased HIF1A stability in villous explants and stimulated transforming growth factor beta 3 (TGFB3) expression consistent with promoter analyses showing that HIF1A transactivates TGFB3. These data demonstrate that during placental development, HIF1A is regulated by temporal and spatial changes in expression and association of molecules forming the multi-protein VHLCBC complex as well as prolyl hydroxylase activities.
Planning for the next pandemic of influenza

Worldwide influenza pandemics have occurred at irregular and unpredictable intervals throughout history and it is confidently expected that they will continue to occur in the future. It is now recognised that these pandemics result when avian influenza A viruses succeed in adaption to and transmission between humans. The impact of pandemic influenza is substantial in terms of morbidity, mortality and economic cost and there is the potential for serious social disruption. Influenza vaccines remain the most effective defence against influenza but will be in short supply during a pandemic, as will the new specific anti‐influenza drugs, due to the lead‐time required for production and rapid spread of the virus. To minimise the impact of pandemics it is imperative to maximise the availability of both vaccines and antivirals and to ensure that they are used optimally. This requires planning at both the international and national levels. The World Health Organization has, therefore, developed a staged plan for responding to a pandemic threat which is based principally on its surveillance program. It has also prepared guidelines to assist national agencies in their planning. However, there may be further options for increasing our preparedness which should also be considered. Copyright © 2001 John Wiley & Sons, Ltd.