Miracle-dz/UniFAR-FTUs huggingface dataset:
Tolerating some redundancy significantly speeds up clustering of large protein databases

MOTIVATION Sequence clustering replaces groups of similar sequences in a database with single representatives. Clustering large protein databases like the NCBI Non-Redundant database (NR) using even the best currently available clustering algorithms is very time-consuming and only practical at relatively high sequence identity thresholds. Our previous program, CD-HI, clustered NR at 90% identity in approximately 1 h and at 75% identity in approximately 1 day on a 1 GHz Linux PC (Li et al., Bioinformatics, 17, 282, 2001); however even faster clustering speed is needed because the size of protein databases are rapidly growing and many applications desire a lower attainable thresholds. RESULTS For our previous algorithm (CD-HI), we have employed short-word filters to speed up the clustering. In this paper, we show that tolerating some redundancy makes for more efficient use of these short-word filters and increases the program's speed 100 times. Our new program implements this technique and clusters NR at 70% identity within 2 h, and at 50% identity in approximately 5 days. Although some redundancy is present after clustering, our new program's results only differ from our previous program's by less than 0.4%.
Organic-Inorganic Hybrid Solar Cells: State of the Art, Challenges and Perspectives

Novel photovoltaic (PV) technologies are currently investigated and evaluated as approaches to contribute to a more environmental friendly energy supply in many countries. One of the driving forces are the aims to reduce the emission of green house gases and the dependency on importing fossil energy resources from political unstable countries. Additionally the wish to replace nuclear power by greener and less threatening technologies will enhance the development of regenerative energy supply in many countries especially after the recent nuclear catastrophe at Fukushima nuclear power plant in Japan in March 2011. This will include the more rapid implementation of existing mature PV technologies but also the development and improvement of novel PV approaches such as organic PV (OPV) and dye-sensitized solar cells (DSSCs) together with new efficient strategies for energy storage and distribution to make electric power, deriving from PVs, available whenever and wherever it is needed. The so-called 1st generation of solar cells based on e.g. bulk crystalline and polycrystalline silicon is still dominating the PV market. However, so-called 2nd generation solar cells mainly consisting out of thin film solar cells based on CdTe, Copper Indium Gallium Selenide (CIGS), and amorphous silicon gained distribution of ca. 25% in market share today worldwide. It is expected that this number will increase significantly within the next years. While for the 1st and 2nd generation solar cells commercial solar panels are available with decent power conversion efficiencies (PCEs) and lifetimes, the emerging 3rd generation solar cells such as OPV and DSSCs technologies are still in the development phase. Some commercially available products have recently entered the market such as e.g. solar bags representing niche products, which are so far not suitable for competing with traditional large scale applications of solar panels of the 1st and 2nd generations. In traditional solar panels the differences between best solar cell and average solar cell efficiencies are much smaller than for the emerging solar cell technologies with the consequence that modules of 3rd generation solar cells still suffer from too low performance. In Table 1 the best cell and module efficiencies of different PV technologies are compared. It has to be mentioned that especially for the emerging new PV technologies the average efficiencies are significantly lower than the results of the best cells.
Rapid and reliable preimplantation genetic diagnosis of common hemoglobin Bart's hydrops fetalis syndrome and hemoglobin H disease determinants using an enhanced single‐tube decaplex polymerase chain reaction assay

immune response, tumor borden, and organ toxicity. Dot blot analysis on mice serum showed the presence of IgG antibodies againt WT1 after vaccination with GST-WT1 protein1AD and GST-WT1 protein alone. By contrast, the antibodies were not present after injection of GST 1AD and PBS. (Fig. 1 panel C and D). Furthermore, cytotoxicity of T cells was evaluated by Cr release test. In mice injected with GST-WT1 protein1AD the level of cytotoxixity was 30%6 2 compared to 2%6 0.5 (background level) in control mice. Finally, we examined the toxixity in organs which physiologically express WT1 al low levels: lymphonode, spleen, ovary, and kidney in vaccinated mice and controls. No toxicity was observed (Fig. 1 panel F). Hemocromocytometric analysis as well as BM smears (data not shown) excluded any kind of hematological toxicity. The mean Hb level was 13.9 gr/dL in vaccinated mice and 14.2 gr/dL in controls (P> 0.05), the median WBC count was 5135/ll in vaccinated mice and 6357//ll in controls (P> 0.05), the median platelet count was 1128000/ll in vaccinated mice and 1020000/ll in controls (P> 0.05). In conclusion, vaccination with WT1 protein induces a significant cytotoxic response and a potent antibody response. This results, at least in mice, in a significant reduction of the tumor borden. The median reduction of the volume of the tumor after 8 weeks of vacciantion is 62%. (Fig. 1 panel B). This strategy may allow to overcome some of the limits associated with peptide vaccination including the restriction of the HLA typing of the patient and the prevalent T CD8 response. This strategy allows to exploit the whole reactive potential of the immune system, both cytotoxic and humoral.
Development and Validation of a Comparative Genomic Fingerprinting Method for High-Resolution Genotyping of Campylobacter jejuni

ABSTRACT Campylobacter spp. are a leading cause of bacterial gastroenteritis worldwide. The need for molecular subtyping methods with enhanced discrimination in the context of surveillance- and outbreak-based epidemiologic investigations of Campylobacter spp. is critical to our understanding of sources and routes of transmission and the development of mitigation strategies to reduce the incidence of campylobacteriosis. We describe the development and validation of a rapid and high-resolution comparative genomic fingerprinting (CGF) method for C. jejuni. A total of 412 isolates from agricultural, environmental, retail, and human clinical sources obtained from the Canadian national integrated enteric pathogen surveillance program (C-EnterNet) were analyzed using a 40-gene assay (CGF40) and multilocus sequence typing (MLST). The significantly higher Simpson's index of diversity (ID) obtained with CGF40 (ID = 0.994) suggests that it has a higher discriminatory power than MLST at both the level of clonal complex (ID = 0.873) and sequence type (ID = 0.935). High Wallace coefficients obtained when CGF40 was used as the primary typing method suggest that CGF and MLST are highly concordant, and we show that isolates with identical MLST profiles are comprised of isolates with distinct but highly similar CGF profiles. The high concordance with MLST coupled with the ability to discriminate between closely related isolates suggests that CFG40 is useful in differentiating highly prevalent sequence types, such as ST21 and ST45. CGF40 is a high-resolution comparative genomics-based method for C. jejuni subtyping with high discriminatory power that is also rapid, low cost, and easily deployable for routine epidemiologic surveillance and outbreak investigations.
Osteoarticular and soft-tissue melioidosis in Malaysia: clinical characteristics and molecular typing of the causative agent.

INTRODUCTION Melioidosis involving bone, joints, and soft tissue is rare and reported usually following dissemination of disease from infection elsewhere in the body; to a lesser degree, it can also be reported as the primary manifestation of melioidosis. METHODOLOGY The orthopedic registry at Hospital University Sains Malaysia from 2008 until 2014 was retrospectively reviewed and was followed by molecular typing of Burkholderia pseudomallei. RESULTS Out of 20 cases identified, 19 patients were confirmed to have osteoarticular and/or soft-tissue melioidosis. The majority of the patients were males (84%), and 16 patients had underlying diabetes mellitus with no significant estimated risk with the disease outcomes. Bacterial genotype was not associated with the disease as a risk. Death was a significant outcome in patients with bacteremic infections (p = 0.044). CONCLUSION Patients with lung or skin melioidosis require careful treatment follow-up to minimize the chance for secondary osteoarticular infection. Human risk factors remain the leading predisposing factors for melioidosis. Early laboratory and clinical diagnosis and acute-phase treatment can decrease morbidity and mortality.
Attachment, Temperament, and Adrenocortical Activity in Infancy. A Study of Psychoendocrine Regulation.

Examined the relations among adrenocortical stress reactivity, infant emotional or proneness-todistress temperament, and quality of attachment in 66 infants tested at 9 and at 13 months. Performed the Louisville Temperament Assessment at 9 months and conducted the Strange Situation at 13 months. Adrenocortical activity was not associated with attachment classifications. Emotional temperament at 9 months was strongly correlated with emotional temperament at 13 months. There was also evidence that at both ages infants who were more prone to distress experienced greater increases in adrenocortical activity during the laboratory tests. Significantly, however, although both the Louisville Temperament Assessment and the Strange Situation involve maternal separation (a potent stimulant of the adrenocortical system in nonhuman primate infants), we noted only small elevations in cortisol, and these elevations were significant only at 9 months.
Nearly Optimal NP-Hardness of Unique Coverage

The Unique Coverage problem, given a universe V of elements and a collection E of subsets of V, asks to find S ⊆ V to maximize the number of e e E that intersects S in exactly one element. When each e e E has cardinality at most k, it is also known as 1-in-k Hitting Set, and admits a simple Ω ([EQUATION])-approximation algorithm. For constant k, we prove that 1-in-k Hitting Set is NP-hard to approximate within a factor O([EQUATION]). This improves the result of Guruswami and Zhou [SODA'11, ToC'12], who proved the same result assuming the Unique Games Conjecture. For Unique Coverage, we prove that it is hard to approximate within a factor O([EQUATION]) for any e > 0, unless NP admits quasipoly-nomial time algorithms. This improves the results of Demaine et al. [SODA'06, SICOMP'08], including their a 1/ log1/3 n inapproximability factor which was proven under the Random 3SAT Hypothesis. Our simple proof combines ideas from two classical inapproximability results for Set Cover and Constraint Satisfaction Problem, made efficient by various derandomization methods based on bounded independence.
Comparing volatility forecasting models during the global financial crisis

ABSTRACT Volatility estimation in financial markets has always been a challenge especially in time of crisis. Once asset prices and investment decisions are highly sensitive to such variable, many different models have been proposed in literature. This article estimates the volatility from a new family of stochastic volatility models called non-Gaussian State Space Models, a subclass of state space models where it is possible to compute exact likelihood. Volatilities of important Asian and Oceanian stock market indexes have been estimated and compared to APARCH model estimates. Results showed that non-Gaussian State Space Models outperformed significantly in both in-sample and forecasting cases.
Flashback: decoupled lightweight wireless control

Unlike their cellular counterparts, Wi-Fi networks do not have the luxury of a dedicated control plane that is decoupled from the data plane. Consequently, Wi-Fi struggles to provide many of the capabilities that are taken for granted in cellular networks, including efficient and fair resource allocation, QoS and handoffs. The reason for the lack of a control plane with designated spectrum is that it would impose significant overhead. This is at odds with Wi-Fi's goal of providing a simple, plug-and-play network. In this paper we present Flashback, a novel technique that provides a decoupled low overhead control plane for wireless networks that retains the simplicity of Wi-Fi's distributed asynchronous operation. Flashback allows nodes to reliably send short control messages concurrently with data transmissions, while ensuring that data packets are decoded correctly without harming throughput. We utilize Flashback's novel messaging capability to design, implement and experimentally evaluate a reliable control plane for Wi-Fi with rates from 175Kbps to 400Kbps depending on the environment. Moreover, to demonstrate its broad applicability, we design and implement a novel resource allocation mechanism that utilizes Flashback to provide efficient, QoS-aware and fair medium access, while eliminating control overheads including data plane contention, RTS/CTS and random back offs.
Estimation of body surface area of extremely obese human subjects.

The body surface areas of one normal and four extremely obese human subjects have been estimated by three methods: a) direct measurement by a method similar to that which Du Bois described; b) calculation from the Du Bois height-weight formula; and c) calculation from the Du Bois linear formula. The values for the total body surface area of the obese subjects calculated from the height-weight formula varied up to 11% below those that were directly measured. The values for the total body surface area obtained with the linear formula ranged between 13% and 20% above the direct measurements, this being almost entirely due to discrepancies in the trunk and in the thigh estimations. It has been concluded that estimation of the body surface area oxf extremely obese subjects by the Du Bois height-weight formula is satisfactory when considered in relation to the accuracy of the physiologic measurements with which it is generally used. Because of the unusual body form the Du Bois linear formula has been found unsatisfactory for this group. Submitted on March 1, 1960
A direct method for 3D factorization of nonrigid motion observed in 2D

The nonrigid structure-from-motion (NSFM) problem seeks to recover a sequence of 3D shapes, shape articulation parameters, and camera view matrices from 2D correspondence data. Factorization approaches relate the principal subspaces of the data matrix to the desired parameters through a linear corrective transform. Current methods for finding this transform are heuristic or depend on strong assumptions about the data. We show how to solve for this transform by directly minimizing deviation from the required orthogonal structure of the projection/articulation matrix. The solution is exact for noiseless data and an order of magnitude more accurate than state-of-the-art methods for noisy data.
Extragalactic optical-infrared background radiation, its time evolution and the cosmic photon-photon opacity

Context. The background radiation in the optical and the infrared cause energy loss in the propagation of high energy particles through space. In particular, TeV observations with Cherenkov telescopes of extragalactic sources are influenced by the opacity effects due to the interaction of the very high-energy source photons with the background light. Aims. With the aim of assessing with the best possible detail these opacity terms, we have modelled the extragalactic optical and infrared backgounds using available information on cosmic sources in the universe from far-UV to sub-millimeter wavelengths over a wide range of cosmic epochs. Methods. We have exploited the relevant cosmological survey data – including number counts, redshift distributions, luminosity functions – from ground-based observatories in the optical, near-IR, and sub-millimeter, as well as multi-wavelength information coming from the HST, ISO and Spitzer space telescopes. Additional constraints have been used from direct measurements or upper limits on the extragalactic backgrounds by dedicated missions (COBE). All data were fitted and interpolated with a multi-wavelength backward evolutionary model, allowing us to estimate the background photon density and its redshift evolution. From the redshift-dependent background spectrum, the photon-photon opacities for sources of high-energy emission at any redshifts were then computed. The same results can also be used to compute the optical depths for any kind of processes in the intergalactic space involving interactions with background photons (like scattering of cosmic-ray particles). Results. We have applied our photon-photon opacity estimates to the analysis of spectral data at TeV energies on a few BLAZARs of particular interest. The opacity-corrected TeV spectra are entirely consistent with standard photon-generation processes and show photon indices steeper than Γintrinsic = 1.6. Contrary to some previous claims, but in agreement with other reports, we find no evidence for any truly diffuse background components in addition to those from resolved sources. We have tested in particular the effects of a photon background originating at very high redshifts, as would be the emissions by a primeval population of Population III stars around z ∼ 10. We could not identify any opacity features in our studied BLAZAR spectra consistent with such an emission and place a stringent limit on such a diffuse photon intensity of ∼ 6n W/m 2 /sr between 1 and 4 μm. Conclusions. TeV observations of BLAZARs are consistent with background radiation contributed by resolved galaxies in the optical and IR, and exclude prominent additional components from very high-z unresolved sources.
Solution Structure of the Circular γ-Domain Analog from the Wheat Metallothionein Ec-1

The first cyclic analog of a metallothionein (MT) was prepared and analyzed by UV and (magnetic) circular dichroism spectroscopy, ESI-MS as well as NMR spectroscopy. Results reveal that the evaluated cyclic γ-Ec-1 domain of the wheat MT Ec-1 retains its ability to coordinate two Zn(II) or Cd(II) ions and adopts a three-dimensional structure that is highly similar to the one of the linear wild-type form. However, the reduced flexibility of the protein backbone facilitates structure solution significantly and results in a certain stabilization of metal binding to the protein.
Serving Society, Repurposing the State: Religious Charity and Resistance in China*

Faith-based charities are among the hundreds of thousands of non-profit, non-state organizations that have emerged in China in recent decades. The social service activities of these groups can rightly be seen as supporting the regime’s policies and long-term goals. Yet faith-based organizations (FBOs) also enable religious adherents to resist aspects of China’s authoritarian system, albeit in subtle and nonconfrontational ways. They do so by expanding the spaces and forms of religious practice beyond the limits imposed by the state, through organizational forms which the state itself has created and approved: the non-profit, non-enterprise unit and the charitable foundation. In transforming the organizations, spaces and behaviors of charity into vehicles of spiritual practice, FBOs “repurpose” the state for religious ends. The repurposing practiced by Chinese religious charities constitutes a distinct mode of subtle, non-contentious resistance.
The primacy effect in memory for repetitions: Evidence for the role of lag between repetitions in source monitoring

The primacy effect in memory for repetitions describes the phenomenon that participants, when presented with repeated items, are more likely to remember attributes of the first presentation than attributes of later repetitions (DiGirolamo & Hintzman, 1997). Interestingly, this effect is assumed to be due to less thorough encoding of the second and later repetitions. This account resembles the explanation typically invoked to explain spacing effects in item memory. Based on the similarity between the accounts of the spacing effect and the primacy effect in memory for repetitions, we suggest that the primacy effect of repetitions should also be moderated by the lag between repetitions. This prediction is tested in two experiments using a source memory paradigm that allows for studying the primacy effect of repetitions, spacing effects in item memory, and source memory in a unified paradigm. The results show that the primacy effect for memory of repetitions occurs at short lags between repetitions but not under long lags.
Classification of Motor Imagery EEG Signals Based on STFTs

Human motor imagery tasks evoke electroencephalogram (EEG) signal changes. We describe a new technique for the classification of motor imagery electroencephalogram (EEG) recordings. The technique is based on a time-frequency analysis of EEG signals, regarding the relations between the EEG data obtained from the C3/C4 electrodes, the features were reduced according the Fisher distance. This reduced feature set is finally fed to a linear discriminant for classification. The algorithm was applied to 3 subjects, the classification performance of the proposed algorithm varied between 70% and 93.1%; across subjects. Keywords-Brain computer interface (BCI); time-frequency analysis; Fisher distance; EEG(electroencephalogram)
The horserace between distractors and targets: Retrieval-based probe responding depends on distractor–target asynchrony

According to models assuming binding of stimulus and response features, any features can be integrated into a compound (consisting of stimulus and response features) and stored in episodic memory, even features irrelevant to the task. Reencountering any part of such an episode can retrieve the entire episode (or “event file”), including the response. That is, even the repeated presentation of a distractor can retrieve a response given to a target stimulus accompanied by this very distractor. We analysed how distractor-induced retrieval of an event-file competes with the response generation process triggered by the target by varying the stimulus onset asynchrony of targets and distractors. In particular, we used a selection task with prime–probe sequences and asynchronous onset of distractors and targets on the probe. Distractor-induced retrieval was only observed if the probe distractor appeared before or simultaneously with the probe target but not if the probe distractor appeared after probe target onset.
Oxygen-sensing PHDs regulate bone homeostasis through the modulation of osteoprotegerin

The contribution of oxygen gradients in regulating bone and blood homeostasis remains unknown. Wu et al. find that HIF activation associated with PHD2 and PHD3 inactivation drove bone accumulation by modulating osteoblastic/osteoclastic cross-talk through the direct regulation of OPG. Combined inactivation of PHD1, PHD2, and PHD3 resulted in extreme HIF-1α/HIF-2α activation, leading to polycythemia and excessive bone accumulation by overstimulating angiogenic–osteogenic coupling. They identify OPG as a HIF target gene capable of directing osteoblast-mediated osteoclastogenesis to regulate bone homeostasis.