Miracle-dz/UniFAR-FTUs huggingface dataset:
Assembling the Marine Metagenome, One Cell at a Time

The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms. We employed fluorescence-activated cell sorting and multiple displacement amplification to obtain hundreds of micrograms of genomic DNA from individual, uncultured cells of two marine flavobacteria from the Gulf of Maine that were phylogenetically distant from existing cultured strains. Shotgun sequencing and genome finishing yielded 1.9 Mbp in 17 contigs and 1.5 Mbp in 21 contigs for the two flavobacteria, with estimated genome recoveries of about 91% and 78%, respectively. Only 0.24% of the assembling sequences were contaminants and were removed from further analysis using rigorous quality control. In contrast to all cultured strains of marine flavobacteria, the two single cell genomes were excellent Global Ocean Sampling (GOS) metagenome fragment recruiters, demonstrating their numerical significance in the ocean. The geographic distribution of GOS recruits along the Northwest Atlantic coast coincided with ocean surface currents. Metabolic reconstruction indicated diverse potential energy sources, including biopolymer degradation, proteorhodopsin photometabolism, and hydrogen oxidation. Compared to cultured relatives, the two uncultured flavobacteria have small genome sizes, few non-coding nucleotides, and few paralogous genes, suggesting adaptations to narrow ecological niches. These features may have contributed to the abundance of the two taxa in specific regions of the ocean, and may have hindered their cultivation. We demonstrate the power of single cell DNA sequencing to generate reference genomes of uncultured taxa from a complex microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa.
Analysis of human samples reveals impaired SHH-dependent cerebellar development in Joubert syndrome/Meckel syndrome

Joubert syndrome (JS) and Meckel syndrome (MKS) are pleiotropic ciliopathies characterized by severe defects of the cerebellar vermis, ranging from hypoplasia to aplasia. Interestingly, ciliary conditional mutant mice have a hypoplastic cerebellum in which the proliferation of cerebellar granule cell progenitors (GCPs) in response to Sonic hedgehog (SHH) is severely reduced. This suggests that Shh signaling defects could contribute to the vermis hypoplasia observed in the human syndromes. As existing JS/MKS mutant mouse models suggest apparently contradictory hypotheses on JS/MKS etiology, we investigated Shh signaling directly on human fetal samples. First, in an examination of human cerebellar development, we linked the rates of GCP proliferation to the different levels and localizations of active Shh signaling and showed that the GCP possessed a primary cilium with CEP290 at its base. Second, we found that the proliferation of GCPs and their response to SHH were severely impaired in the cerebellum of subjects with JS/MKS and Jeune syndrome. Finally, we showed that the defect in GCP proliferation was similar in the cerebellar vermis and hemispheres in all patients with ciliopathy analyzed, suggesting that the specific cause of vermal hypo-/aplasia precedes this defect. Our results, obtained from the analysis of human samples, show that the hemispheres and the vermis are affected in JS/MKS and provide evidence of a defective cellular mechanism in these pathologic processes.
Aspects of Multisensory Perception: The Integration of Visual and Auditory Information in Musical Experiences

Abstract: One of the requirements for being a successful musical conductor is to be able to locate sounds instantaneously in time and space. Because this requires the integration of auditory and visual information, the purpose of this study was to examine multisensory processing in conductors and a matched set of control subjects. Subjects participated in a series of behavioral tasks, including pitch discrimination, temporal‐order judgment (TOJ), and target localization. Additionally, fMRI scans were done on a subset of subjects who performed a multisensory TOJ task. Analyses of behavioral data indicate that, in the auditory realm, conductors were more accurate in both pitch discrimination and TOJs as well as in locating targets in space. Furthermore, these same subjects also demonstrated a benefit from the combination of auditory and visual information that was not observed in control subjects when locating visual targets. Finally, neural substrates in BA 37, 39/40 were identified as potential areas underlying the conductors' superior multisensory TOJs. Data collection and analyses are ongoing and will lead to an improved understanding of multisensory integration in a complex, musical behavior.
On the Low SNR Capacity of MIMO Fading Channels With Imperfect Channel State Information

The capacity of multiple-input multiple-output (MIMO) Rayleigh fading channels with full knowledge of channel state information (CSI) at both the transmitter and the receiver (CSI-TR) has been shown recently to scale at low signal-to-noise ratio (SNR) essentially as SNR log(1/SNR), independently of the number of transmit and receive antennas. In this paper, we investigate the ergodic capacity of MIMO Rayleigh fading channel with estimated channel state information at the transmitter (CSI-T) and possibly imperfect channel state information at the receiver (CSI-R). Our framework can be seen as a generalization of previous works as it can capture the perfect CSI-TR as a special case when the estimation error variance goes to zero. In this paper, we mainly focus on the low SNR regime, and we show that the capacity scales as (1 - α) SNR log(1/SNR), where α is the estimation error variance. This characterization shows the loss of performance due to error estimation over the perfect channel state information at both the transmitter and the receiver. As a by-product of our new analysis, we show that our framework can be also extended to characterize the capacity of MIMO Rician fading channels at low SNR with possibly imperfect CSI-T and CSI-R.
Psychotic-Like Experiences, Appraisals, and Trauma

This study examined some of the predictions made by cognitive models of psychosis, specifically the potential contribution of appraisals and trauma to the development of “need for care. ” Two groups reporting psychotic-like experiences with and without a “need for care” were compared on types of experiences, appraisals of these experiences, distress, and trauma. Both groups reported similar overall levels of psychotic-like experiences, but were characterized by distinct types of experiences. The clinical group was more distressed, endorsed more externalizing and personalizing appraisals, and fewer psychological/normalizing apraisals of their experiences than the nonclinical group. Both groups showed high rates of trauma, and interpersonal trauma was associated with more personalizing and fewer psychological/normalizing appraisals. These results suggest that “need for care” is characterized by distress and personalizing appraisals, but not by a higher incidence of trauma. The role of interpersonal trauma, specifically, may be to predispose to a “paranoid” world view.
ISOLATION AND CHARACTERIZATION OF SUBCELLULAR MEMBRANES OF E N T A

A method is described for the isolation of subcellular membranes of Entamoeba invadens. Plasma membranes were obtained by rate centrifugation followed by isopycnic centrifugation on a sucrose gradient. Intact phagolysosomes floated in a 10% sucrose solution providing a simple technique for isolation. Phagolysosomal membranes were collected by isopycnic centrifugation, after lysis of the phagolysosomes. Microsomes were obtained by differential centrifugation. Membrane fractions were examined by electron microscopy, and the contamination of each fraction was determined with marker enzymes. Mg2+-ATPase is associated with the plasma membrane. Acid phosphatase (/3-glycerophosphate) was associated mainly with phagolysosomal membranes. Plasma membranes also contained acid phosphatase activity which hydrolyzes p-nitrophenylphosphate but not fl-glycerophosphate. The localization of the two phosphatases was confirmed cytochemically. Isolated plasma membranes were contaminated with phagolysosomal membranes (15%) and with microsomes (25%). No more than 5% of the phagolysosomal membrane fraction consisted of plasma membranes. Contamination of the microsomes by plasma and phagolysosomal membranes was 10% and 7%, respectively. Plasma membranes and phagolysosomal membranes had a high ratio of cholesterol to phospholipid (0.93 and 1.05 /xmol/#mol, respectively). Microsomes were relatively poor in cholesterol (0.39 /~mol//zmol). Microsomes, plasma, and phagolysosomal membranes contained increasing amounts of sphingolipids (12%, 17%, and 28%). Phagolysosomal membranes had a high percentage of phosphatidylserine but little phosphatidylcholine. Microsomes were rich in phosphatidylcholine (45%). Differences in phospholipid composition between plasma and phagolysosomal membranes are discussed in view of the phagocytic process. Electron micrographs of Entamoeba reveal the relatively simple structure of these protozoan cells (Fig. 1). The main organelles are the phagolysosomes (31,32) which are scattered throughout the cell. A nucleus is present as well as a Golgi apparatus (9, 30) and endoplasmic reticulum (22, 23, ThE JOURNAL OF CELL BIOLOGY" VOLUME 71, 1976 9 pages 357-369 357 on N ovem er 7, 2017 jcb.rress. org D ow nladed fom
The Effects of Transcranial Direct Current Stimulation (tDCS) on Multitasking Throughput Capacity

Background: Multitasking has become an integral attribute associated with military operations within the past several decades. As the amount of information that needs to be processed during these high level multitasking environments exceeds the human operators' capabilities, the information throughput capacity reaches an asymptotic limit. At this point, the human operator can no longer effectively process and respond to the incoming information resulting in a plateau or decline in performance. The objective of the study was to evaluate the efficacy of a non-invasive brain stimulation technique known as transcranial direct current stimulation (tDCS) applied to a scalp location over the left dorsolateral prefrontal cortex (lDLPFC) to improve information processing capabilities during a multitasking environment. Methods: The study consisted of 20 participants from Wright-Patterson Air Force Base (16 male and 4 female) with an average age of 31.1 (SD = 4.5). Participants were randomly assigned into two groups, each consisting of eight males and two females. Group one received 2 mA of anodal tDCS and group two received sham tDCS over the lDLPFC on their testing day. Results: The findings indicate that anodal tDCS significantly improves the participants' information processing capability resulting in improved performance compared to sham tDCS. For example, the multitasking throughput capacity for the sham tDCS group plateaued near 1.0 bits/s at the higher baud input (2.0 bits/s) whereas the anodal tDCS group plateaued near 1.3 bits/s. Conclusion: The findings provided new evidence that tDCS has the ability to augment and enhance multitasking capability in a human operator. Future research should be conducted to determine the longevity of the enhancement of transcranial direct current stimulation on multitasking performance, which has yet to be accomplished.
Autonomous environment manipulation to assist humanoid locomotion

Legged robots have unique capabilities to traverse complex environments by stepping over and onto objects. Many footstep planners have been developed to take advantage of these capabilities. However, legged robots also have inherent constraints such as a maximum step height and distance. These constraints typically limit their reachable space, independent of footstep planning. Thus, we propose that robots such as humanoid robots that have manipulation capabilities should use them. A robot should autonomously modify its environment if necessary. We present a system that enabled a real robot to use a box to create itself a stair step or place a board on the ground to cross a gap, allowing it to reach its otherwise unreachable goal configuration.
Genetics of Alcohol Dependence: A Review of Clinical Studies

Background/Aims: Alcohol dependence is a common severe psychiatric disorder with a multifactorial etiology. Since the completion of the human genome project and with the increased availability of high-throughput genotyping, multiple genetic risk factors for substance-related disorders, including alcohol dependence, have been identified, but not all results could be replicated. Methods: We systematically review the clinical literature on genetic risk factors for alcohol dependence and alcohol-related phenotypes, including candidate gene-based studies, linkage studies and genome-wide association studies (GWAS). Results: Irrespectively of the methodology employed, the most robust findings regarding genetic risk factors for alcohol dependence concern genetic variations that affect alcohol metabolism. GWAS confirm the importance of the alcohol dehydrogenase gene cluster on chromosome 4 in the genetic risk for alcohol dependence with multiple variants that exert a small, but cumulative influence. A single variant with strong influence on individual risk is the aldehyde dehydrogenase 2 ALDHD2*2 variant common in Asian populations. Other robust associations have been found with previously uncharacterized genes like KIAA0040, and such observations can lead to the identification of thus far unknown signaling pathways. Converging evidence also points to a role of glutamatergic, dopaminergic and serotonergic neurotransmitter signaling in the risk for alcohol dependence, but effects are small, and gene-environment interactions further increase the complexity. Conclusion: With few exceptions like ALDH2*2, the contribution of individual genetic variants to the risk for alcohol-related disorders is small. However, the concentration of risk variants within neurotransmitter signaling pathways may help to deepen our understanding of the underlying pathophysiology and thereby contribute to develop novel therapeutic strategies.
Adaptive TDD UL/DL slot utilization for cellular controlled D2D communications

Cellular controlled Device-to-Device (D2D) system is a local service for future communication systems like LTE, LTE-A, etc. D2D communications can share the Uplink (UL) or Downlink (DL) resources with cellular communications to improve system throughput. Since reusing UL resource or DL resource has different merits in different scenarios, if D2D only reuses either UL or DL resource during the whole communication procedure, there may be some problems, such as load balance, interference, etc. This paper proposes a method for adaptively TDD UL/DL slot utilization for D2D communications according to the change of scenario in TD-LTE system. Analysis is made for illustrating our novel method and the advantages are listed.
Fast and Globally Convergent Pose Estimation from Video Images

Determining the rigid transformation relating 2D images to known 3D geometry is a classical problem in photogrammetry and computer vision. Heretofore, the best methods for solving the problem have relied on iterative optimization methods which cannot be proven to converge and/or which do not effectively account for the orthonormal structure of rotation matrices. We show that the pose estimation problem can be formulated as that of minimizing an error metric based on collinearity in object (as opposed to image) space. Using object space collinearity error, we derive an iterative algorithm which directly computes orthogonal rotation matrices and which is globally convergent. Experimentally, we show that the method is computationally efficient, that it is no less accurate than the best currently employed optimization methods, and that it outperforms all tested methods in robustness to outliers.
Epidemiological studies of Serratia marcescens infections by bacteriocin (marcescin) typing.

NASU, M. Epidemiological Studies of Serratia marcescens Infections by Bacteriocin (Marcescin) Typing. Tohoku J. exp. Med., 1981, 133 (1), 45-52 -Serratia marcescens strains isolated from various clinical materials and the environment in Nagasaki University Hospital during the period from April 1970 to May 1979 were classified by bacteriocin (marcescin) production typing by means of the agar cross streaking method utilizing 8 indicators without induction. Six hundred and fifty-four isolated strains (406 from urine, 153 from sputum, 60 from pus & exudate, 13 from bile and 21 from others) in the above period were classified into 30 types by bacteriocin production typing. The distribution of the bacteriocin type of these strains differed according to the clinical material. Epidemiological investigations were performed using the isolates obtained from different patients and places in the Hospital during the 15 month period from January 1975 to March 1976. Each ward had a distinctive distribution of the bacteriocin type of the isolates. The bacterial flora in 100 sites of each ward was examined, and 5 strains of Serratia marcescens were obtained from the Gynecological Ward (4 from a washing recess, 1 from a treatment room) and 5 from the Urological Ward (2 from a floor, 1 from a bed). The bacteriocin types of these strains were coincident with that of the isolated from the patients admitted to both wards except one strain from the treatment room of the Gynecological Ward. Six patients were studied for comparison of the bacteriocin types of Serratia marcescens isolated from several materials taken from the same patients. Three of these patients demonstrated identical bacteriocin type strains in different materials, but the others showed different bacteriocin types of Serratia marcescens. Furthermore, the communicable form of Serratia marcescens among the hospitalized patients was classified by bacteriocin production typing.
Immunotherapy alleviates amyloid-associated synaptic pathology in an Alzheimer’s disease mouse model

Accumulation of amyloid-beta leads to loss of functional synapses in Alzheimer’s disease. Dorostkar et al. report that immunotherapy against oligomeric amyloid-beta in the Tg2576 mouse model attenuates synapse loss near plaques, and abolishes it elsewhere. Sequestering oligomeric amyloid-beta may counteract synaptic pathology, even while fibrillar amyloid load remains unchanged.
The Impact of Symptom Interpretation on Physician Utilization

This article explores physician consultation decisions among a sample of elderly people living in community settings. The analysis integrates the insights of research on illness behavior, particularly symptom interpretation and lay consultation, with previous specifications of the Health Behavior Model. Data were gathered through personal interviews and health diaries completed on a daily basis for 21 consecutive days by a probability sample of older people living in community settings. Results indicate that uncertainty regarding potential seriousness, level of pain or interference, and causal attributions were the most consistently significant predictors of physician contact.
Gabor wavelet based features for medical image analysis and classification

Identifying relevant, representative and more important, discriminant image features for analysis and proper image classification purpose is one of the main tasks in image processing and pattern recognition field. In this paper, Gabor wavelets based features are extracted from medical mammogram images representing normal tissues, or benign and malign tumors. Once features are detected, Principal Component Analysis (PCA) is further employed to reduce data dimensionality. To an end, directional properties and frequency spectrum of those features are analyzed with respect to the classification performance by employing multiclass support vector machines as classifier. For comparison, as baseline, PCA was also applied directly to the data set with no feature filtering. The experimental results indicate that directional properties of Gabor wavelets provided by their orientation are important issues to accurately discriminate mammogram tumor types.
Rule induction for adaptive sport video characterization using MLN clause templates

The grounding of high-level semantic concepts is a key requirement of video annotation systems. Rule induction can thus constitute an invaluable intermediate step in characterizing protocol-governed domains, such as broadcast sports footage. We here set out a novel “clause grammar template” approach to the problem of rule-induction in video footage of court games that employs a second-order meta-grammar for Markov Logic Network construction. The aim is to build an adaptive system for sports video annotation capable, in principle, both of learning ab initio and also adaptively transferring learning between distinct rule domains. The method is tested with respect to both a simulated game predicate generator and also real data derived from tennis footage via computer-vision based approaches including HOG3D based player-action classification, Hough-transform-based court detection, and graph-theoretic ball-tracking. Experiments demonstrate that the method exhibits both error resilience and learning transfer in the court domain context. Moreover the clause template approach naturally generalizes to any suitably-constrained, protocol-governed video domain characterized by feature noise or detector error. keywords: Video Annotation, Markov processes, Stochastic Logic, Markov logic network (MLN), Action Recognition, Behavior discovery, Statistical Relational Reasoning
Increased frequency of isolated cleft palate in infants exposed to lamotrigine during pregnancy

INCREASED FREQUENCY OF ISOLATED CLEFT PALATE IN INFANTS EXPOSED TO LAMOTRIGINE DURING PREGNANCY To the Editor: We read with interest the findings of Holmes et al.1 of an increased risk of oral clefts in offspring exposed to lamotrigine (LTG) during pregnancy. Our results from the UK Epilepsy & Pregnancy Register, another independent prospective registration and follow-up study, do not confirm this finding. Our study methods have been previously published.2 We had full outcome data for 1,229 pregnancies exposed to LTG as monotherapy, resulting in 1,151 live births. Twenty-eight major congenital malformations were reported (MCM rate 2.4% [95% confidence interval (CI) 1.7– 3.5]). Of these, one male infant was born with nonsyndromic cleft lip and palate (0.087% [95% CI 0.015–0.49]) to a 23-year-old nonsmoker, having been exposed to 200 mg/day of LTG through pregnancy. Folic acid was commenced following conception. There were no cases of isolated cleft lip or isolated cleft palate. No specific pattern of malformations has emerged in this cohort. A European network of population-based congenital anomaly registers (EUROCAT) did not find any evidence of an increased risk of isolated oral clefts relative to other malformations due to first trimester exposure to LTG in monotherapy.3 We congratulate Holmes et al. on their work, but the substantial differences between their and our findings highlights the difficulty in interpreting data from observational uncontrolled studies especially when the event rates studied are rare. While there may be true differences for oral clefts between the populations studied in the United States and the United Kingdom, it is also possible that the differences reflect reporting bias. Despite all the pregnancy data available, there are still major problems in counseling women with epilepsy. Replication across different datasets is likely to be critical before we are fully able to inform women.