Miracle-dz/UniFAR-FTUs huggingface dataset:
The “Miserable Minority” Following Mild Traumatic Brain Injury: Who Are They and do Meta-Analyses Hide Them?

Ruff et al. (1994; Ruff, Camenzuli, & Mueller, 1996) hypothesized that some mild traumatic brain injury (MTBI) patients will suffer chronic symptomatic complaints and impairments, identifying this subgroup as the “miserable minority. ” However, several meta-analyses of the effects of MTBI have been published (e.g., Rohling et al., 2011) showing no significant cognitive impairments following recovery. Recently Pertab, James, and Bigler (2009) suggested that meta-analysis might be obscuring impairments in some MTBI patients, presenting a hypothetical score distribution to illustrate their claim. Our statistical analyses of their hypothetical figure and of several other potential distributions containing an impaired subgroup that varied as a function of effect size and base rate of occurrence did not support the existence of a miserable minority that is obscured in meta-analyses by the larger group of MTBI patients experiencing full recovery. Indeed, given our recent published MTBI effect size of −0.07 (Rohling et al., 2011), for an impaired subgroup to exist, the level of impairment would have to be just under a tenth of a standard deviation, equivalent to a WMS-IV Index score value of 1 point. At effect sizes this small, any cut score chosen on a test to diagnose patients would result in more false positives than true positives. This greatly increases the risk of misdiagnosis in persons who are susceptible to misattribution, expectancy effects, and “diagnosis threat,” thereby increasing the risk of iatrogenic illness.
Genetic dissection of lupus pathogenesis: a recipe for nephrophilic autoantibodies.

Sle1 and Sle3 are 2 loci that confer susceptibility to lupus nephritis in the NZM2410 strain of mice. Our previous work has shown that B6.NZMc1 mice, congenic for Sle1, exhibit loss of tolerance to chromatin but do not develop any pathogenic autoantibodies or disease. B6.NZMc7 mice, congenic for Sle3, exhibit low-grade polyclonal B- and T-cell activation, elevated CD4/CD8 ratios, and mildly penetrant glomerulonephritis. In contrast to these monocongenics, the present study reveals that B6.NZMc1|c7 mice, bicongenic for Sle1 and Sle3, exhibit splenomegaly, significantly expanded populations of activated B and CD4(+) T cells, and a robust, variegated IgG autoantibody response targeting multiple components of chromatin (including double-stranded DNA), intact glomeruli, and basement membrane matrix antigens. As one might predict, these mice, particularly the females, exhibit highly penetrant glomerulonephritis. These findings lend strong support to a two-step epistatic model for the formation of pathogenic, nephrophilic autoantibodies in lupus. Whereas loci such as Sle1 may serve to breach tolerance to chromatin, full-blown pathogenic maturation of the autoantibody response appears to require additional input from other loci (such as Sle3) and gender-based factors.
MS/MS networking guided analysis of molecule and gene cluster families

Significance The paper introduces the concepts of molecular families (MFs) and gene cluster families (GCFs). We define MFs as structurally related molecules based on their mass spectral fragmentation patterns, whereas GCFs are biosynthetic gene clusters that show similar gene cluster organization with a high degree of sequence similarity. We use MS/MS networking as a tool to map the molecular network of more than 60 organisms, most of which are unsequenced, and locate their nonribosomal peptide MFs. These MFs from unsequenced organisms are then connected to GCFs of publicly available genome sequences of closely related organisms. The ability to correlate the production of specialized metabolites to the genetic capacity of the organism that produces such molecules has become an invaluable tool in aiding the discovery of biotechnologically applicable molecules. Here, we accomplish this task by matching molecular families with gene cluster families, making these correlations to 60 microbes at one time instead of connecting one molecule to one organism at a time, such as how it is traditionally done. We can correlate these families through the use of nanospray desorption electrospray ionization MS/MS, an ambient pressure MS technique, in conjunction with MS/MS networking and peptidogenomics. We matched the molecular families of peptide natural products produced by 42 bacilli and 18 pseudomonads through the generation of amino acid sequence tags from MS/MS data of specific clusters found in the MS/MS network. These sequence tags were then linked to biosynthetic gene clusters in publicly accessible genomes, providing us with the ability to link particular molecules with the genes that produced them. As an example of its use, this approach was applied to two unsequenced Pseudoalteromonas species, leading to the discovery of the gene cluster for a molecular family, the bromoalterochromides, in the previously sequenced strain P. piscicida JCM 20779T. The approach itself is not limited to 60 related strains, because spectral networking can be readily adopted to look at molecular family–gene cluster families of hundreds or more diverse organisms in one single MS/MS network.
Lambing rate using vitrified blastocysts is improved by culture with BSA and hyaluronan

Fatty acid‐free bovine serum albumin (BSAFAF) can be added to supplement medium used in the culture of sheep embryos. BSAFAF was able to support blastocyst and subsequent embryo development at rates equivalent to that of fetal calf serum (FCS)‐supplemented medium when fresh embryos were transferred. Furthermore, culture with BSAFAF significantly increased development of vitrified blastocysts transferred into synchronized sheep. The addition of the glycosaminoglycan, hyaluronan (HA) to the culture medium in the third and fifth day also increased cryo‐tolerance of blastocysts and in turn lambing rate was improved. Mol. Reprod. Dev. 74: 42–47, 2007. © 2006 Wiley‐Liss, Inc.
Immunohistochemical evaluation of interface membranes from failed cemented and uncemented acetabular components.

Aseptic loosening of acetabular components is a primary factor compromising the long-term outcome of cemented and cementless total hip replacement. It is unknown whether the pathogenesis of the loosening process is identical for both types of fixation. The specific aim of this study was to determine whether there is a difference in the cellular and cytokine profiles of interface membranes removed from between the implant and the host bone from failed cemented (n = 5) and failed cementless acetabulae (n = 5). Routine histology and immunohistochemical evaluations were completed on each tissue specimen. The monoclonal antibodies used included those specific for cell types (macrophages, fibroblasts, T lymphocytes) and for cytokines (IL-1beta, IL-6, TNF-alpha). The patients were all revised for loosening. The time to revision was significantly longer for the cemented group (16.6 yr; 13-21 range) than for the cementless group (8.9 yr; 4-13 range). In all cases, slides from each group stained positively for each of the cell types and cytokines evaluated. Immunohistochemical analyses indicated a predominance of macrophages and ubiquitous staining for the cytokines IL-1beta and TNF-alpha within the membranes of both patient groups. The intensities of cytokine staining were similar for both patient groups. More regions of fibroblastic connective tissue were observed surrounding failed cementless components as compared to those of the cemented group. The clinical ramification of our findings is that, despite differences in the cellular composition of the periprosthetic membranes, the membranes from failed cemented and cementless implants contain cytokines, which have been shown to be capable of modulating the inflammatory response. These inflammatory mediators are likely to play a significant role in the development of osteolysis and prosthetic loosening.
Dual vortex theory of strongly interacting electrons: A non-Fermi liquid with a twist

As discovered in the quantum Hall effect, a very effective way for strongly repulsive electrons to minimize their potential energy is to aquire nonzero relative angular momentum. We pursue this mechanism for interacting two-dimensional electrons in zero magnetic field, by employing a representation of the electrons as composite bosons interacting with a Chern-Simons gauge field. This enables us to construct a dual description in which the fundamental constituents are vortices in the auxiliary boson fields. The resulting formalism embraces a cornucopia of possible phases. Remarkably, superconductivity is a generic feature, while the Fermi liquid is not. We identify a dual Z2 symmetry which, when broken ~unbroken! , leads to spin-charge confinement ~separation! Many aspects of our earlier discussions of the nodal liquid find surprising incarnations in this new framework.
Identifying Cognate Sets Across Dictionaries of Related Languages

We present a system for identifying cognate sets across dictionaries of related languages. The likelihood of a cognate relationship is calculated on the basis of a rich set of features that capture both phonetic and semantic similarity, as well as the presence of regular sound correspondences. The similarity scores are used to cluster words from different languages that may originate from a common proto-word. When tested on the Algonquian language family, our system detects 63% of cognate sets while maintaining cluster purity of 70%.
Stoppage of blood flow in 3-methylcholanthrene-induced autochthonous primary tumor due to a novel combretastatin A-4 derivative, AC7700, and its antitumor effect.

BACKGROUND Using several transplanted tumors in rats and mice, we have recently shown that the acute extensive necrosis of tumor nodules is caused by the systemic administration of AC7700, a novel combretastatin A-4 derivative, and that the necrosis can be attributed to irreversible stoppage of tumor blood flow (TBF). In this study, the antivascular and antitumor effects of AC7700 were tested on primary autochthonous tumor. MATERIAL AND METHODS Primary sarcomas were induced in Fischer F344 rats by a single s.c. inoculation of 3-methylcholanthrene (MC) (4 mg/0.5 ml/head). Changes in TBF due to AC7700 were measured by hydrogen clearance technique. Antitumor effects of AC7700 were evaluated by histology and tumor growth inhibition. RESULTS The earliest primary tumor appeared 77 days after MC treatment and the last tumor appeared after 273 days (median, 140 days). Once tumors occurred, they continued to grow slowly and never regressed spontaneously. The mean doubling time of tumors (n = 34) during exponential growth was 12.6 +/- 9.0 days (mean +/- SD) (range, 5.4-55.9 days). Blood flow in these slow-growing autochthonous tumors decreased highly significantly from 25.2 +/- 15.5 to 4.4 +/- 3.2 ml/min/100 g (24 electrodes)(P < 0.001) within 30 min due to rapid i.v. injection (0.15 ml/min) of 10 mg/kg AC7700 and the decreased TBF did not recover during the experimental period of 6 h. On the other hand, TBF did not change significantly due to 0.9% NaCl solution (10 electrodes). In addition, TBF immediately began to decrease following slow infusion (0.005 ml/min) of 10 mg/kg AC7700 and decreased by approximately 80% (12 electrodes) at 20 min after the start of AC7700 infusion. To evaluate the antitumor effect of AC7700 on the primary tumors, 10 mg/kg AC7700 was injected i.v. to tumor-bearing rats. Although in the natural course, such tumors never stop growing, the tumor growth was strongly inhibited by AC700 (n = 5). In 2 cases, tumors never regrew for the observation period of 45 days. Biopsy and histological findings (n = 5) showed that tumors underwent extensive necrosis, as was observed previously for transplanted tumors following AC7700 administration. CONCLUSION From the present experiment it was demonstrated not only in transplanted tumors but also in carcinogen-induced autochthonous primary tumors that acute and sustained stoppage of TBF led to strong antitumor effects. The novel anticancer compound AC7700 might become a very useful therapeutic strategy against refractory cancers.
Overview of the Marine Roseobacter Lineage

Despite the overwhelming bacterial diversity present in the world's oceans, the majority of recognized marine bacteria fall into as few as nine major clades (36), many of which have yet to be cultivated in the laboratory. Molecular-based approaches targeting 16S rRNA genes demonstrate that the Roseobacter clade is one of these major marine groups, typically comprising upwards of 20% of coastal and 15% of mixed-layer ocean bacterioplankton communities (see, e.g., references 36, 37, 42, 98, and 109). Roseobacters are well represented across diverse marine habitats, from coastal to open oceans and from sea ice to sea floor (see, e.g., references 16, 28, 37, 42, 52, and 98). Members have been found to be free living, particle associated, or in commensal relationships with marine phytoplankton, invertebrates, and vertebrates (see, e.g., references 4, 6, 7, 44, 49, 115, and 119). Furthermore, representatives of the clade stand out as representing one of the most readily cultivated of the major marine lineages (36). These isolated representatives are serving as the foundation for an improved understanding of marine bacterial ecology and physiology.
Continuing Education: Multi-modality Brain Tumor Imaging – MRI, PET, and PET/MRI

Imaging plays a pivotal role in the clinical management of human brain tumors. Diagnostic anatomical features such as the presence (or absence) of contrast enhancement, hemorrhage, calcification and/or macroscopic necrosis are readily assessed through standard magnetic resonance imaging (MRI) and computed tomography (CT). Secondary pathologic conditions such as mass effect, edema and herniation are also assessed via CT and MRI. Serial imaging with gadolinium-enhanced MRI is routinely employed to evaluate the success or failure of therapy, and for post-therapy surveillance in order to detect early tumor recurrence. Advanced MRI techniques and positron emission tomography (PET) imaging offer physiologic, metabolic or functional information about tumor biology that goes beyond the diagnostic yield of standard MRI and CT imaging. Each individual advanced MRI modality, including MR perfusion, MR diffusion, and MR spectroscopy techniques, and each individual PET radiotracer, beginning with FDG and including multiple tracers for tumor cellular proliferation, hypoxia and amino acid transport, reveals important information about different aspects of brain tumor metabolism. With the advent of combined PET-MRI scanners, we have entered an era wherein the relationships among different elements of tumor metabolism can be simultaneously explored through multimodality MRI and PET imaging. The purpose of this review is to provide a practical and clinically-relevant overview of current anatomic and physiologic imaging of brain tumors as a foundation for further investigations, with a primary focus on MRI and PET techniques that have demonstrated utility or have shown early promise through published clinical trials in the current care of brain tumor patients.
Testing a level of response to alcohol-based model of heavy drinking and alcohol problems in 1,905 17-year-olds.

BACKGROUND The low level of response (LR) to alcohol is one of several genetically influenced characteristics that increase the risk for heavy drinking and alcohol problems. Efforts to understand how LR operates through additional life influences have been carried out primarily in modest-sized U.S.-based samples with limited statistical power, raising questions about generalizability and about the importance of components with smaller effects. This study evaluates a full LR-based model of risk in a large sample of adolescents from the United Kingdom. METHODS Cross-sectional structural equation models were used for the approximate first half of the age 17 subjects assessed by the Avon Longitudinal Study of Parents and Children, generating data on 1,905 adolescents (mean age 17.8 years, 44.2% boys). LR was measured with the Self-Rating of the Effects of Alcohol Questionnaire, outcomes were based on drinking quantities and problems, and standardized questionnaires were used to evaluate peer substance use, alcohol expectancies, and using alcohol to cope with stress. RESULTS In this young and large U.K. sample, a low LR related to more adverse alcohol outcomes both directly and through partial mediation by all 3 additional key variables (peer substance use, expectancies, and coping). The models were similar in boys and girls. CONCLUSIONS These results confirm key elements of the hypothesized LR-based model in a large U.K. sample, supporting some generalizability beyond U.S. groups. They also indicate that with enough statistical power, multiple elements contribute to how LR relates to alcohol outcomes and reinforce the applicability of the model to both genders.
Preferential Relative Porphyrin Enrichment in Solar Keratoses upon Topical Application of ^‐Aminolevulinic Acid Methylester

Topically applied δ‐aminolevulinic acid is used efficiently for the treatment of solar keratoses by photodynamic therapy. Recent animal studies suggest that porphyrin sensitization of epithelial tissue is improved by using esters rather than free δ‐aminolevulinic acid. The present study examines porphyrin metabolite formation after topical application of δ‐aminolevulinic acid or δ‐aminolevulinic acid methylester in human solar keratoses versus adjacent normal skin. Levels of total porphyrins, porphyrin metabolites and protein were measured in skin samples excised after 1 and 6 h. Higher levels of porphyrins were observed in solar keratoses than in normal skin with both substances. Maximum porphyrin levels were present in solar keratoses treated with δ‐aminolevulinic acid for 6 h. However, the ratio of porphyrins in solar keratoses versus adjacent normal skin was higher with 8‐aminolevulinic acid methylester. The pattern of porphyrins showed no significant difference between normal and afflicted skin, protoporphyrin being predominant. The results suggest that application of free δ‐aminolevulinic acid may be more effective in sensitizing solar keratoses. However, treatment with 8‐aminolevulinic acid methylester leads to a preferential enrichment of porphyrins within lesional skin.
Three Recurrent Neural Networks and Three Numerical Methods for Solving a Repetitive Motion Planning Scheme of Redundant Robot Manipulators

Three neural networks and three numerical methods are investigated, developed, and compared to solve a repetitive motion planning (RMP) scheme for remedying joint-drift problems of redundant robot manipulators. Three recurrent neural networks, i.e., a dual neural network, a linear variational inequality (LVI)-based primal-dual neural network, and a simplified LVI-based primal-dual neural network, are recurrent and real time, and they do not need to be trained in advance. Three numerical methods, i.e., the 94LVI method, the E47 method, and the M4 method, are time discrete and ready to conduct in digital computers. All these solutions have global linear convergence. Computer simulations and physical robot experiments verify that they are all effective to solve the RMP scheme. The comparisons show that neural networks are more accurate and faster than numerical methods on the same simulated condition under the majority normal circumstances. Furthermore, numerical methods are easy to be applied in digital computers since they are time discrete.
A quantitative study on information contribution of prosody phrase boundaries in Chinese speech

In speech, acoustic cues are used to manifest a number of linguistic events including segmental phonemes and supra-segmental ones such as tones, prosodic phrasing structure, intonation, etc. It has been an interesting topic to quantitatively compare the importance of different linguistic events. However, previous studies have been mainly confined to segmental or segment-like units. No studies could be found to show quantitatively the importance of supra-segmental events of prosody boundaries. From the view of information transmission, both segmental and supra-segmental events make indispensable contributions to natural human speech communication. This paper presents a novel way to quantitatively estimate the information contribution of prosody boundaries, taking the same way to estimate those of segmental phonetic contrasts and syllable tones. Experiments were done using a Chinese newspaper text corpus and a conversation speech corpus. Preliminary results show that prosody boundaries carry much more information than phonetic segments. Hence, they are much more important than segments for human speech communication.
Combined evaluation of Rad51 and ERCC1 expressions for sensitivity to platinum agents in non‐small cell lung cancer

DNA repair enzyme expression in tumor cells possibly affects sensitivity to anti‐cancer agents. The aim of this study was to determine the relationship between expression status of DNA repair enzymes and chemosensitivity in patients with non‐small cell lung cancer (NSCLC). NSCLC tissues prepared from the surgical specimens of 41 patients were subjected to immunohistochemical analysis for Rad51 and ERCC1 proteins and to a chemosensitivity test using the MTT assay. The relationships between the expression status of the DNA repair enzymes and ex vivo chemosensitivity to various agents were evaluated. A positive expression for Rad51 and ERCC1 was observed in 17 cases (41%) and 20 cases (49%), respectively. The positivity of Rad51 was closely related to a certain histologic type of squamous cell carcinoma and poor differentiation, and the positivity of ERCC1 tended to be related to squamous cell carcinoma. In chemosensitivity tests, sensitivities to CDDP and CBDCA were significantly lower when both 2 enzymes were positive (p = 0.012 and 0.04 in CDDP, 0.014 and 0.03 in CBDCA). Both Rad51 and ERCC1 expressions showed no significant relationship with sensitivities to paclitaxel, etoposide, vinorelbine, gemcitabine, 5‐FU, or irinotecan. In conclusion, combined expression of Rad51 and ERCC1 expression is associated with resistance to platinum agents in the ex vivo study of clinical NSCLC, and evaluation of expression status of both DNA repair enzymes would be a predictor for clinical response to platinum‐based chemotherapies. © 2007 Wiley‐Liss, Inc.