Miracle-dz/UniFAR-FTUs huggingface dataset:
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

The identification of untranslated regions, introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genome and demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed. We confirmed many known and predicted introns and demonstrated that others are not actively used. Alternative initiation codons and upstream open reading frames also were identified for many yeast genes. We also found unexpected 3′-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated.
Structural Basis for Specific Substrate Recognition by the Chloroplast Signal Recognition Particle Protein cpSRP43

Secretory and membrane proteins carry amino-terminal signal sequences that, in cotranslational targeting, are recognized by the signal recognition particle protein SRP54 without sequence specificity. The most abundant membrane proteins on Earth are the light-harvesting chlorophyll a/b binding proteins (LHCPs). They are synthesized in the cytoplasm, imported into the chloroplast, and posttranslationally targeted to the thylakoid membrane by cpSRP, a heterodimer formed by cpSRP54 and cpSRP43. We present the 1.5 angstrom crystal structure of cpSRP43 characterized by a unique arrangement of chromodomains and ankyrin repeats. The overall shape and charge distribution of cpSRP43 resembles the SRP RNA, which is absent in chloroplasts. The complex with the internal signal sequence of LHCPs reveals that cpSRP43 specifically recognizes a DPLG peptide motif. We describe how cpSPR43 adapts the universally conserved SRP system to posttranslational targeting and insertion of the LHCP family of membrane proteins.
Predicting Firm Success From the Facial Appearance of Chief Executive Officers of Non-Profit Organizations

Recent research has demonstrated that judgments of Chief Executive Officers’ (CEOs’) faces predict their firms’ financial performance, finding that characteristics associated with higher power (e.g., dominance) predict greater profits. Most of these studies have focused on CEOs of profit-based businesses, where the main criterion for success is financial gain. Here, we examined whether facial appearance might predict measures of success in a sample of CEOs of non-profit organizations (NPOs). Indeed, contrary to findings for the CEOs of profit-based businesses, judgments of leadership and power from the faces of CEOs of NPOs negatively correlated with multiple measures of charitable success (Study 1). Moreover, CEOs of NPOs looked less powerful than the CEOs of profit-based businesses (Study 2) and leadership ratings positively associated with warmth-based traits and NPO success when participants knew the faces belonged to CEOs of NPOs (Study 3). CEOs who look less dominant may therefore achieve greater success in leading NPOs, opposite the relationship found for the CEOs of profit-based companies. Thus, the relationship between facial appearance and leadership success varies by organizational context.
Brief Report: Dclk1 Deletion in Tuft Cells Results in Impaired Epithelial Repair After Radiation Injury

The role of Dclk1+ tuft cells in the replacement of intestinal epithelia and reestablishing the epithelial barrier after severe genotoxic insult is completely unknown. Successful restoration requires precise coordination between the cells within each crypt subunit. While the mechanisms that control this response remain largely uncertain, the radiation model remains an exceptional surrogate for stem cell‐associated crypt loss. Following the creation of Dclk1‐intestinal‐epithelial‐deficient Villin‐Cre;Dclk1flox/flox mice, widespread gene expression changes were detected in isolated intestinal epithelia during homeostasis. While the number of surviving crypts was unaffected, Villin‐Cre;Dclk1flox/flox mice failed to maintain tight junctions and died at approximately 5 days, where Dclk1flox/flox mice lived until day 10 following radiation injury. These findings suggest that Dclk1 plays a functional role critical in the epithelial restorative response. Stem Cells 2014;32:822–827
Olfactory Training Using Heavy and Light Weight Molecule Odors

Background Repeated short-term exposure to odors is known to improve olfaction in patients with acquired olfactory dysfunction. The aim was to find out whether differences in molecular weight of odors used for olfactory training influences olfaction. We hypothesized a greater improvement following training with light weight molecule (LWM) odors. Methods A prospective study was performed in patients with posttraumatic (PTOL) and postviral olfactory loss (PVOL). Olfactory training was performed over a period of 5 months. One group (n = 48) used four odors containing heavy weight molecules (HWM; >150 g/mol) and another (n = 48) containing LWM (<150 g/mol). Olfaction was tested before and after the training using the Sniffin’ Sticks test. Results Olfactory training was associated with olfactory improvement, with the improvement in PVOL patients being three times greater than that seen in the PTOL group. Compared with LWM training, HWM training was associated with a significantly greater improvement in Phenyl Ethyl Alcohol (PEA) threshold scores in PVOL patients; however, no such improvement could be shown for other subtests or in PTOL patients. Conclusion Overall, training was associated with olfactory improvement. With the exception of threshold scores in PVOL, there were no significant differences between LWM and HWM groups.
Graphene: Status and Prospects

Expanding Flatland Since its discovery and isolation some 5 years ago, research on graphene has exploded. The sheets of carbon atoms, just one atom thick, exhibit a vast array of properties—mechanical, optical, and electrical—that make it an ideal test bed to probe fundamental problems in physics, as well as lending itself to a wide portfolio of applications. Geim (p. 1530), the discoverer of this remarkable material, reviews recent advances and discusses what other developments may be in store for this material. Graphene is a wonder material with many superlatives to its name. It is the thinnest known material in the universe and the strongest ever measured. Its charge carriers exhibit giant intrinsic mobility, have zero effective mass, and can travel for micrometers without scattering at room temperature. Graphene can sustain current densities six orders of magnitude higher than that of copper, shows record thermal conductivity and stiffness, is impermeable to gases, and reconciles such conflicting qualities as brittleness and ductility. Electron transport in graphene is described by a Dirac-like equation, which allows the investigation of relativistic quantum phenomena in a benchtop experiment. This review analyzes recent trends in graphene research and applications, and attempts to identify future directions in which the field is likely to develop.
Putative periodontal and teeth in pathogens on titanium implants and teeth in experimental gingivitis and periodontitis in beagle dogs

: The microflora around titanium implants and teeth in 4 beagle dogs was analyzed in order to follow the longitudinal development from healthy conditions to experimental gingivitis and periodontitis. A 2-month plaque control program was performed to establish healthy conditions on titanium implants and control teeth (baseline, day 0). Subgingival bacterial samples and radiographs were obtained. The plaque control was ceased and all measurements were repeated on day 21 (gingivitis). A new period of plaque control was initiated to re-establish healthy conditions (day 49). A cotton ligature was placed subgingivally around the implants and the control teeth to induce tissue breakdown. The ligatures were removed on day 91. The study was completed with registrations on day 121 (periodontitis). No significant microbiological difference was found between titanium implants and teeth in healthy conditions and in gingivitis and periodontitis. The mean total viable count increased 10 times on implants as well as on teeth. Streptococci were dominating at baseline: 40.2% on implants and 60.6% on teeth and decreased in gingivitis to 11.7% and 5.4%. When periodontitis had developed, the proportion of streptococci was < 1%. At baseline few Porphyromonas gingivalis and Prevotella intermedia were detected. They increased at gingivitis to 37.4% and 21.0%; when periodontitis developed, they comprised about 25.0%. Microbial colonization and establishment on titanium implants with healthy gingiva, experimental gingivitis and periodontitis follow the same pattern as on teeth.
For Your Local Eyes Only: Culture-Specific Face Typicality Influences Perceptions of Trustworthiness

Recent findings show that typical faces are judged as more trustworthy than atypical faces. However, it is not clear whether employment of typicality cues in trustworthiness judgment happens across cultures and if these cues are culture specific. In two studies, conducted in Japan and Israel, participants judged trustworthiness and attractiveness of faces. In Study 1, faces varied along a cross-cultural dimension ranging from a Japanese to an Israeli typical face. Own-culture typical faces were perceived as more trustworthy than other-culture typical faces, suggesting that people in both cultures employ typicality cues when judging trustworthiness, but that the cues, indicative of typicality, are culture dependent. Because perceivers may be less familiar with other-culture typicality cues, Study 2 tested the extent to which they rely on available facial information other than typicality, when judging other-culture faces. In Study 2, Japanese and Israeli faces varied from either Japanese or Israeli attractive to unattractive with the respective typical face at the midpoint. For own-culture faces, trustworthiness judgments peaked around own-culture typical face. However, when judging other-culture faces, both cultures also employed attractiveness cues, but this effect was more apparent for Japanese participants. Our findings highlight the importance of culture when considering the effect of typicality on trustworthiness judgments.
Smoke Invigoration Versus Inhibition of Clouds over the Amazon

The effect of anthropogenic aerosols on clouds is one of the most important and least understood aspects of human-induced climate change. Small changes in the amount of cloud coverage can produce a climate forcing equivalent in magnitude and opposite in sign to that caused by anthropogenic greenhouse gases, and changes in cloud height can shift the effect of clouds from cooling to warming. Focusing on the Amazon, we show a smooth transition between two opposing effects of aerosols on clouds: the microphysical and the radiative. We show how a feedback between the optical properties of aerosols and the cloud fraction can modify the aerosol forcing, changing the total radiative energy and redistributing it over the atmospheric column.
Own Attractiveness and Dissatisfaction With Physical Appearance Independently Predict the Salience of Facial Cues to Size When Women Judge Other Women’s Attractiveness

While facial cues to body size are a valid guide to health and attractiveness, it is unclear whether the observer’s own condition predicts the salience of (low) size as a cue to female attractiveness. The current study examines whether measures related to women’s own attractiveness/appearance predict the extent to which they use facial cues to size to differentiate other women on the attractiveness dimension. Women completed a body mass index (BMI) preference task, where they indicated their preference for high- versus low-BMI versions of the same woman, provided data to calculate their BMI and completed various psychometric measures (self-rated attractiveness/health, dissatisfaction with physical appearance). Here, attractive women and women who were dissatisfied with their own appearance were more likely to associate facial cues to low body size with high attractiveness. These data suggest that psychological factors related to women’s appearance shape their evaluations of other women based on cues to size. Such variation in attractiveness judgements may function to reduce the costs of female competition for resources, for example, by identifying “quality” rivals or excluding others based on cues to size.
Dissociating Higher and Lower Order Visual Motion Systems by Priming Illusory Apparent Motion

Motion processing is thought of as a hierarchical system composed of higher and lower order components. Past research has shown that these components can be dissociated using motion priming paradigms in which the lower order system produces negative priming while the higher order system produces positive priming. By manipulating various stimulus parameters, researchers have probed these two systems using bistable test stimuli that permit only two motion interpretations. Here we employ maximally ambiguous test stimuli composed of randomly refreshing pixels in a task that allows observers to report more than just two types of motion percepts. We show that even with such stimuli, motion priming can constrain the unstructured random pixel patterns into coherent percepts of positive or negative apparent motion. Moreover, we find that the higher order system is uniquely susceptible to cognitive influences, as evidenced by a significant suppression of positive priming in the presence of alternative response options.
Skin Conductance Responses to Masked Emotional Faces Are Modulated by Hit Rate but Not Signal Detection Theory Adjustments for Subjective Differences in the Detection Threshold

The biological preparedness model suggests that survival-related visual cues elicit physiological changes without awareness to enable us to respond to our environment. Previous studies have reported some evidence for this effect. In the current article, we argue that this evidence is subject to methodological confounds. These include the use of a universal masked presentation threshold, the employment of hit rates (HRs) to measure meta-awareness, and the assertion of overall guess-level target detection using nonsignificance. In the current report, we address these issues and test whether masked emotional faces can elicit changes in physiology. We present participants with subjectively adjusted masked angry, fearful, happy, and neutral faces using HRs and signal detection theory. We assess detection performance using a strict Bayesian criterion for meta-awareness. Our findings reveal that HR adjustments in the detection threshold allow higher skin conductance responses to happy, fearful, and angry faces, but that this effect could not be reported by the same participants when the adjustments were made using signal detection measures. Combined these findings suggest that very brief biologically relevant stimuli can elicit physiological changes but cast doubt to the extent that this effect can occur in response to truly unconscious emotional faces.
Seven ‘deadly’ assumptions: unravelling the implications of HIV/AIDS among grandmothers in South Africa and beyond

ABSTRACT Over the past few years, the pivotal roles older women play in responding to the unprecedented HIV/AIDS epidemic in southern Africa has received increasing recognition by academics, governments, funding agencies, non-governmental organisations, and citizens around the world. Yet, discourses surrounding AIDS and ‘grandmotherhood’ are laden with a number of ungrounded assumptions that have important implications for researchers, advocates and decision-makers. Drawing on ethnographic and survey data predominantly from South Africa, this paper challenges seven such assumptions. The paper illustrates how certain prevailing ‘wisdoms’ about grandmothers and AIDS in southern Africa are not entirely accurate and may mask many women's struggles and vulnerabilities, perpetuate stereotypes and misguide well-meaning policies. It also suggests that the societal impacts of AIDS in the region are, at present, not as dramatic as often portrayed, largely because the strength and resilience of many older women have cushioned some of the negative consequences. The paper thus calls for more nuanced and forward-looking analyses and interventions – ones that recognise grandmothers as central to the society's thin safety net and that grapple with older women's complex and diverse vulnerabilities.
Binary convolutional neural network on RRAM

Recent progress in the machine learning field makes low bit-level Convolutional Neural Networks (CNNs), even CNNs with binary weights and binary neurons, achieve satisfying recognition accuracy on ImageNet dataset. Binary CNNs (BCNNs) make it possible for introducing low bit-level RRAM devices and low bit-level ADC/DAC interfaces in RRAM-based Computing System (RCS) design, which leads to faster read-and-write operations and better energy efficiency than before. However, some design challenges still exist: (1) how to make matrix splitting when one crossbar is not large enough to hold all parameters of one layer; (2) how to design the pipeline to accelerate the whole CNN forward process. In this paper, an RRAM crossbar-based accelerator is proposed for BCNN forward process. Moreover, the special design for BCNN is well discussed, especially the matrix splitting problem and the pipeline implementation. In our experiment, BCNNs on RRAM show much smaller accuracy loss than multi-bit CNNs for LeNet on MNIST when considering device variation. For AlexNet on ImageNet, the RRAM-based BCNN accelerator saves 58.2% energy consumption and 56.8% area compared with multi-bit CNN structure.
The taste machine: Sense, subjectivity, and statistics in the California wine world

This article is about mid-20th-century attempts to turn subjective judgments about the quality and composition of wine into objective knowledge. It focuses on the research of Maynard Amerine at the University of California, Davis, and his project to formalize the procedures of sensory evaluation. Using controlled experimental conditions, Amerine and colleagues transcribed judgments about taste into numbers that could then be aggregated and analyzed statistically. Through such techniques, they claimed to be able to turn subjectivities into objectivities, rendering private taste sensations into reliable and stable facts about objects in the world.
A speech enhancement approach E-CMN/CSS for speech recognition in car environments

This paper proposes the robust speech enhancement approach E-CMN (Exact Cepstrum Mean Normalization)/CSS (Continuous Spectral Subtraction). The E-CMN, which we proposed for compensation of multiplicative distortions (Shozakai et al., 1997), calculates two cepstrum mean vectors, one for speech for each speaker and the other for non-speech for each environment. The CSS subtracts continuously average spectra at every frame. A high robustness of the proposed method is clarified by comparative evaluation with alternative methods for speech recognition tasks in car environments.
Wnt/β‐Catenin Signaling Is Required to Rescue Midbrain Dopaminergic Progenitors and Promote Neurorepair in Ageing Mouse Model of Parkinson's Disease

Wnt/β‐catenin signaling is required for specification and neurogenesis of midbrain dopaminergic (mDA) neurons, the pivotal neuronal population that degenerates in Parkinson's disease (PD), and in 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) mouse model of PD. Wnt/β‐catenin signaling plays a vital role in adult neurogenesis but whether it might engage DA neurogenesis/neurorepair in the affected PD brain is yet unresolved. Recently, the adult midbrain aqueduct periventricular regions (Aq‐PVRs) were shown to harbor multipotent clonogenic neural stem/progenitor cells (mNPCs) with DA potential in vitro, but restrictive mechanisms in vivo are believed to limit their DA regenerative capacity. Using in vitro mNPC culture systems we herein demonstrate that aging is one most critical factor restricting mNPC neurogenic potential via dysregulation of Wnt/β‐catenin signaling. Coculture paradigms between young/aged (Y/A) mNPCs and Y/A astrocytes identified glial age and a decline of glial‐derived factors including Wnts as key determinants of impaired neurogenic potential, whereas Wnt activation regimens efficiently reversed the diminished proliferative, neuronal, and DA differentiation potential of A‐mNPCs. Next, in vivo studies in wild (Wt) and transgenic β‐catenin reporter mice uncovered Wnt/β‐catenin signaling activation and remarkable astrocyte remodeling of Aq‐PVR in response to MPTP‐induced DA neuron death. Spatio‐temporal analyses unveiled β‐catenin signaling in predopaminergic (Nurr1+/TH−) and imperiled or rescuing DAT+ neurons during MPTP‐induced DA neuron injury and self‐repair. Aging inhibited Wnt signaling, whereas β‐catenin activation in situ with a specific GSK‐3β antagonist promoted a significant degree of DA neurorestoration associated with reversal of motor deficit, with implications for neurorestorative approaches in PD. Stem Cells 2014;32:2147–2163
Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland

The Paleo-Eskimo Saqqaq and Independence I cultures, documented from archaeological remains in Northern Canada and Greenland, represent the earliest human expansion into the New World's northern extremes. However, their origin and genetic relationship to later cultures are unknown. We sequenced a mitochondrial genome from a Paleo-Eskimo human by using 3400-to 4500-year-old frozen hair excavated from an early Greenlandic Saqqaq settlement. The sample is distinct from modern Native Americans and Neo-Eskimos, falling within haplogroup D2a1, a group previously observed among modern Aleuts and Siberian Sireniki Yuit. This result suggests that the earliest migrants into the New World's northern extremes derived from populations in the Bering Sea area and were not directly related to Native Americans or the later Neo-Eskimos that replaced them.
Introducing Transcription Factors to Multipotent Mesenchymal Stem Cells: Making Transdifferentiation Possible

Multipotent mesenchymal stem cells (MSCs) represent a promising autologous source for regenerative medicine. Because MSCs can be isolated from adult tissues, they represent an attractive cell source for autologous transplantation. A straightforward therapeutic strategy in the field of stem cell‐based regenerative medicine is the transplantation of functional differentiated cells as cell replacement for the lost or defective cells affected by disease. However, this strategy requires the capacity to regulate stem cell differentiation toward the desired cell fate. This therapeutic approach assumes the capability to direct MSC differentiation toward diverse cell fates, including those outside the mesenchymal lineage, a process termed transdifferentiation. The capacity of MSCs to undergo functional transdifferentiation has been questioned over the years. Nonetheless, recent studies support that genetic manipulation can serve to promote transdifferentiation. Specifically, forced expression of certain transcription factors can lead to reprogramming and alter cell fate. Using such a method, fully differentiated lymphocytes have been reprogrammed to become macrophages and, remarkably, somatic cells have been reprogrammed to become embryonic stem‐like cells. In this review, we discuss the past and current research aimed at transdifferentiating MSCs, a process with applications that could revolutionize regenerative medicine. STEM CELLS 2009;27:2509–2515