Miracle-dz/UniFAR-FTUs huggingface dataset:
Unexplored Archaeal Diversity in the Great Ape Gut Microbiome

Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis for further studies on the role of archaea in the gut microbiome. ABSTRACT Archaea are habitual residents of the human gut flora but are detected at substantially lower frequencies than bacteria. Previous studies have indicated that each human harbors very few archaeal species. However, the low diversity of human-associated archaea that has been detected could be due to the preponderance of bacteria in these communities, such that relatively few sequences are classified as Archaea even when microbiomes are sampled deeply. Moreover, the universal prokaryotic primer pair typically used to interrogate microbial diversity has low specificity to the archaeal domain, potentially leaving vast amounts of diversity unobserved. As a result, the prevalence, diversity, and distribution of archaea may be substantially underestimated. Here we evaluate archaeal diversity in gut microbiomes using an approach that targets virtually all known members of this domain. Comparing microbiomes across five great ape species allowed us to examine the dynamics of archaeal lineages over evolutionary time scales. These analyses revealed hundreds of gut-associated archaeal lineages, indicating that upwards of 90% of the archaeal diversity in the human and great ape gut microbiomes has been overlooked. Additionally, these results indicate a progressive reduction in archaeal diversity in the human lineage, paralleling the decline reported for bacteria. IMPORTANCE Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis for further studies on the role of archaea in the gut microbiome.
Nonparametric Statistics for Stochastic Processes: Estimation and Prediction

Synopsis. - 1. Inequalities for mixing processes. - 2. Density estimation for discrete time processes. - 3. Regression estimation and prediction for discrete time processes. - 4. Kernel density estimation for continuous time processes. - 5. Regression estimation and prediction in continuous time. - 6. The local time density estimator. - 7. Implementation of nonparametric method and numerical applications. - References.
Learning to Embed Seen/Unseen Compositions based on Graph Networks

Composability allows known concepts to form newer and more complex ones. This coupling process is the research interests of Compositional Zero-Shot Learning (CZSL). The goal can be described as building a classifier for unknown compositions in the testing set based on known attribute primitives (e.g., old, cute) and object primitives (e.g., cats, cars) in the training set. There are many challenges in this process. For example, the same attribute primitive behaves significantly distinct on different objects. Common CZSL methods introduce auxiliary classification information into the model by using the pretrained model or external knowledge base, but the distribution of introduced auxiliary information is usually inconsistent with the distribution of the class information contained in training set itself, resulting in the model's misunderstanding of combined features. In view of this deficiency, we proposed a novel Compositional Graph Convolutional Network model, which consists of two embedding networks for image and label text modal data respectively. With graph convolutional networks, we can eliminate potential differences in information distribution in the pre-training data. Besides, we add a quintuplet loss to cross-entropy loss to generate a smoother feature representation. The results on three benchmarks including MIT-States, UT-Zappos and C-GQA datasets show that the proposed model exceeds the seven state-of-the-art methods in terms of Area Under the Curve (AUC) and classification accuracy. This confirms that our method can generate more recognizable compositional features.
Integral equation techniques: From microwaves, over mm waves, to IR and optical frequencies

Computational electromagnetics has become a real cornerstone in the design of microwave and millimeter wave components and systems. One of the major computational techniques used in these designs is to solve integral equations with the Method of Moments (MoM). Traditionally, MoM has been used extensively for antennas, transmission lines, filters, couplers, etc., mainly in the MHz and GHz range. However, MoM can also be applied at much higher frequencies. It will be shown that at these frequencies, this computational technique is just emerging. One of the reasons is that there are serious differences with the classical implementations, which prohibits the direct use of the well-known commercially available MoM solvers. For example, one of the differences is the fact that the concept of a surface current, confined to a very thin layer at the surface of a conductor, is not valid any more. In this presentation, the different computational techniques will be reviewed and compared, not only in the traditional microwave and millimeter wave range, but especially at THz, IR, and optical frequencies. In concreto, the MAGMAS MoM solver will be compared to a numerical FDTD solver well-known in the plasmonics research community: Lumerical. It will be shown that also at these very high frequencies, MoM has its proper place in the pallet of computational algorithms.
Assessing adverse childhood experiences in chronic pain: it does matter.

To the Editor: In her introduction to a ‘‘special topic series,’’ Karen Raphael questions the purported relationship between childhood abuse and chronic pain in adulthood and expresses doubts about the clinical utility of routinely assessing abuse histories in these patients because—in the author’s opinion—the implications for treatment or course of illness are unclear. As a clinical researcher, I am grateful for Raphael’s rigorous analysis of the (lack of) scientific evidence linking childhood abuse to pain later in adulthood. However, as a pain clinician, I strongly disagree with her clinical advice and arguments. Raphael disregards the fact that childhood victimization experiences not only increase the risk of psychiatric comorbidity in patients with chronic pain (such as depression and substance abuse) but also often lay the groundwork for severe personality disturbances, as a consequence of insecure attachment. Notably, borderline or passive-dependent personality disorders may impede adaptive coping, make the therapeutic relationship ambiguous or conflict laden, and carry the risk of negative countertransference reactions by the caregiver. Therefore, it seems to be crucial to recognize these personality aspects, their interactional correlates, and biographical breeding ground to optimize pain management, therefore, to customize it to these patients’ specific vulnerabilities and needs. Evidently, exploring the patients’ life story is not the same as giving them a questionnaire for scientific purposes. In clinical practice, one should never ‘‘routinely’’ ask about abuse experiences stricto sensu. Instead, nonintrusive questions such as ‘‘how did you feel at home as a child? ’’ or ‘‘how was the relationship between your parents? ’’ may bring up the issue of possible childhood stress and allow patients to disclose relevant information when they feel ready to do so. In sum, researchers should make clinicians aware of methodological pitfalls to prevent them from overestimating anecdotal observations and drawing overhasty conclusions in their daily work. But, eventually, clinicians are in the best position to decide which diagnostic and therapeutic strategies are appropriate to provide optimal help for those who suffer.
EFFECT OF LEAD EXCESS IN SOIL ON THE ACCUMULATION OF P, K AND Na IN INFECTED BY FUSARIUM OXYSPORUM F. SP. RADICIS-LYCOPERSICI IN TOMATO (LYCOPERSICON ESCULENTUM MILL.) PLANTS

S. MANEVA, S. , T. VATCHEV and E. MITEVA, 2013. Effect of lead excess in soil on the accumulation of P, K and Na in infected by Fusarium oxysporum f. sp. radicis-lycopersici in tomato (Lycopersicon esculentum Mill.) plants. Bulg. J. Agric. Sci., 19: 972-980 Pot experiments were conducted in greenhouse of IPAZR, “N. Poushkarov”, Sofia, to study the effects of excess lead (Pb) in soils on the uptake of P, K and Na in tomato plants (Lycopersicon esculentum Mill.), cv. Ideal, grown in Fusarium. oxysporum f. sp. radicis-lycopersici (FORl) infected soils. Lead at the rate of 0, 80 and 160 mg kg -1 soil were added in soil in solution form as lead nitrate [Pb(NO
A longitudinal study of Vero cytotoxin producing Escherichia coli in cattle calves in Sri Lanka

SUMMARY Two cohorts of 10 and 16 calves were followed at weekly or fortnightly intervals from 4–28 and 1–9 weeks respectively to determine whether natural infection by Vero cytotoxin (VT) producing Escherichia coli (VTEC) occurred. Ninety-one of 171 (53%) faecal specimens were VTEC positive and 20–80% of animals at any given time excreted VTEC. Of 104 VTEC strains studied further, 6 different serogroups (O 22.H16; O 25.H5; O 49.H−; O 86.H26; O 88.H25; O 153.H12) and an untypable strain (O ? .H21) were identified. All strains belonging to the same serotype had identical profiles of reactivity with DNA probes to toxins VT1 or 2, LT1 or iI and a probe (CVD419) derived from a plasmid carried by enterohaemorrhagic Escherichia coli O 157.H7. Four of these serotypes were found in the faecal flora of the calves, taken as a group, throughout the 4-month study period. Sixty percent of the strains hybridized with the probe for VT1, 4% with the probe for VT2, and 36% with both probes. Faecal VTEC were significantly associated with overt diarrhoeal illness in animals < 10 weeks of age, but no characteristic profile of markers (serotype or hybridization pattern) in E. coli isolates was associated with diarrhoea. A serological response to VTl was detected in some animals, but faecal VT1 VTEC excretion persisted in spite of seroconversion. VTl seroconversion was not associated with diarrhoea. A serological response to VT2 was not detected even in those animals excreting VT2 VTEC in the faeces.
Ultrastructure of Presumed “Candidatus Rickettsia Andeanae” in Amblyomma maculatum (Acari: Ixodidae)

ABSTRACT Amblyomma maculatum Koch, 1844 (also known as the Gulf Coast tick) is found in parts of the Americas, including the central and southern United States. Its primary importance is as the vector of Rickettsia parkeri, a spotted fever group rickettsia that causes an illness similar to, but milder than, Rocky Mountain spotted fever. A second spotted fever group rickettsia, “Candidatus Rickettsia andeanae,” was detected in Gulf Coast ticks approximately 10 yr ago. However, the significance of this organism, including pathogenicity, has not yet been well-characterized. Here, we use transmission electron microscopy to describe bacteria within the tissues of A. maculatum ticks that were positive by polymerase chain reaction assay for “Ca. R. andeanae. ” In ultrathin sections of unfed A. maculatum adult females, we found evidence of bacteria with morphological features consistent with spotted fever group rickettsiae, including small size (≈0.3 by 0.9 µm), a halo zone (electron-lucent layer around the bacterium), and a trilaminar cell wall. In female ticks, bacteria were present in granular salivary glands and ducts, foregut, Malpighian tubules, nerve trunks, and reproductive tissue. These findings demonstrate evidence of “Ca. R. andeanae” in situ and contribute to our understanding of this novel rickettsia in A. maculatum.
Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants

Significance Terpenoids are ubiquitous products made by land plants with diverse biological functions. Their formation in seed plants is catalyzed by typical plant terpene synthases (TPSs), a well-characterized group of enzymes. In contrast, our knowledge of terpenoid biosynthesis in nonseed plants is very limited. By systematically analyzing the transcriptomes and/or genomes of more than 1000 plant species, we report that microbial terpene synthase-like genes, which are only distantly related to typical plant TPS genes, are widely distributed in nonseed plants, but virtually absent in seed plants. The study provides insights into the evolution of TPS genes in early land plants and opens the door to investigating the diversity and functions of terpenoids in nonseed plants. The vast abundance of terpene natural products in nature is due to enzymes known as terpene synthases (TPSs) that convert acyclic prenyl diphosphate precursors into a multitude of cyclic and acyclic carbon skeletons. Yet the evolution of TPSs is not well understood at higher levels of classification. Microbial TPSs from bacteria and fungi are only distantly related to typical plant TPSs, whereas genes similar to microbial TPS genes have been recently identified in the lycophyte Selaginella moellendorffii. The goal of this study was to investigate the distribution, evolution, and biochemical functions of microbial terpene synthase-like (MTPSL) genes in other plants. By analyzing the transcriptomes of 1,103 plant species ranging from green algae to flowering plants, putative MTPSL genes were identified predominantly from nonseed plants, including liverworts, mosses, hornworts, lycophytes, and monilophytes. Directed searching for MTPSL genes in the sequenced genomes of a wide range of seed plants confirmed their general absence in this group. Among themselves, MTPSL proteins from nonseed plants form four major groups, with two of these more closely related to bacterial TPSs and the other two to fungal TPSs. Two of the four groups contain a canonical aspartate-rich “DDxxD” motif. The third group has a “DDxxxD” motif, and the fourth group has only the first two “DD” conserved in this motif. Upon heterologous expression, representative members from each of the four groups displayed diverse catalytic functions as monoterpene and sesquiterpene synthases, suggesting these are important for terpene formation in nonseed plants.
Enhanced Arteriogenesis and Wound Repair in Dystrophin-Deficient mdx Mice

Background—The absence of functional dystrophin in Duchenne muscular dystrophy (DMD) patients and in mdx mice results in progressive muscle degeneration associated with necrosis, fibrosis, and inflammation. Because vascular supply plays a key role in tissue repair, we examined whether new blood vessel development was altered in mdx mice. Methods and Results—In a model of hindlimb ischemia on femoral artery dissection, hindlimb perfusion, measured by laser Doppler imaging, was higher in mdx mice (0.67±0.26) than in wild-type (WT) mice (0.33±0.18, P<0.03). In keeping with these data, a significant increase in arteriole length density was found in mdx mice (13.6±8.4 mm/mm3) compared with WT mice (7.8±4.6 mm/mm3, P<0.03). Conversely, no difference was observed in capillary density between mice of the 2 genotypes. The enhanced regenerative response was not limited to ischemic skeletal muscle, because in a wound-healing assay, mdx mice showed an accelerated wound closure rate compared with WT mice. Moreover, a vascularization assay in Matrigel plugs containing basic fibroblast growth factor injected subcutaneously revealed an increased length density of arterioles in mdx (46.9±14.7 mm/mm3) versus WT mice (19.5±5.8 mm/mm3, P<0.001). Finally, serum derived from mdx mice sustained formation of endothelium-derived tubular structures in vitro more efficiently than WT serum. Conclusions—These results demonstrate that arteriogenesis is enhanced in mdx mice both after ischemia and skin wounding and in response to growth factors.
Fixed-Polynomial Size Circuit Bounds

In 1982, Kannan showed that $\Sigma^\P_2$ does not have $n^k$-sized circuits for any $k$. Do smaller classes also admit such circuit lower bounds? Despite several improvements of Kannan's result, we still cannot prove that $\P^\NP$ does not have linear size circuits. Work of Aaronson and Wigderson provides strong evidence -- the ``algebrization'' barrier -- that current techniques have inherent limitations in this respect. We explore questions about fixed-polynomial size circuit lower bounds around and beyond the algebrization barrier. We find several connections, including \begin{itemize} \item The following are equivalent: \begin{itemize} \item $\NP$ is in $\SIZE(n^k)$ (has $O(n^k)$-size circuit families) for some $k$ \item For each $c$, $\P^{\NP[n^c]}$ is in $\SIZE(n^k)$ for some $k$ \item $\ONP/1$ is in $\SIZE(n^k)$ for some $k$, where $\ONP$ is the class of languages accepted {\it obliviously} by $\NP$ machines, with witnesses for ``yes'' instances depending only on the input length. \end{itemize} \item For a large number of natural classes ${\cal C}$ and all $k \geq 1$, ${\cal C}$ is in $\SIZE(n^k)$ if and only if ${\cal C}/1\cap\P/\poly$ is in $\SIZE(n^k)$. \item If there is a $d$ such that $\MATIME(n) \subseteq \NTIME(n^d)$, then $\P^{\NP}$ does not have $O(n^k)$ size circuits for any $k ≫ 0$. \item One cannot show $n^2$-size circuit lower bounds for $\oplus \P$ without new nonrelativizing techniques. In particular, the proof that $\PP \not\subseteq \SIZE(n^k)$ for all $k$ relies on the (relativizing) result that $\P^{\PP} \subseteq \MA \Longrightarrow \PP \not\subseteq \SIZE(n^k)$, and we give an oracle relative to which $\P^{\oplus \P} \subseteq \MA$ and $\oplus \P \subseteq \SIZE(n^2)$ both hold. \end{itemize}
Strictly non-blocking WDM cross-connects

Using (WDM) technology, an optical network can route multiple signals simultaneously along a single optical fiber by encoding each signal on its own wavelength. If the network contains places where multiple fibers connect together and signals are allowed to be moved from any of the incoming fibers to any of the outgoing fibers, then the network is said to contain cross-connects. More precisely, a $k_1\,\times\,k_2$ WDM cross-connect has k1 input fibers and k2 output fibers. Each of the k1 input fibers supports the same n1 input wavelengths and each of the k2 output fibers supports the same n2 output wavelengths. Since a signal on input wavelength $\lambda$ can be routed from its input fiber to an output fiber such that it arrives on the output fiber using wavelength $\gamma$, where $\lambda \neq \gamma$, the cross-connect must be capable of performing wavelength conversion. Along any fiber in the cross-connect a device called a wavelength interchanger can be inserted to perform wavelength conversion. In other words if the path of a signal from an input fiber to an output fiber passes through a \wins, then the wavelength of the signal can be changed to any wavelength that is not already in use along the fiber leaving the wavelength interchanger. Given the high cost of \wisns, the overall cost of a \CC{k_1}{k_2} is minimized by reducing the number of \wis in the cross-connect. However, a desirable property for a cross-connect C is for C to always be able to provide a route (and wavelength conversion) for any valid demand from any pair of input and output fibers regardless of the routes of other demands currently routed in C. If C has this capability then it is said to be strictly nonblocking. For most of this paper we consider a demand to be a request for a connection from an input fiber to an output fiber such that the connection starts on a specified input wavelength and leaves the c on a second specified wavelength. Using this demand model, we consider cross-connects for which $k_1$ is not necessarily equal to $k_2$ and the number $n_1$ of supported input wavelengths can differ from the number $n_2$ of supported output wavelengths. Without loss of generality we assume that $k_1 \leq k_2$ and present a family of \snob \CCns{k_1}{k_2}s that use \Opt \wisns. For the case when $k_1 = k_2=k$ and $n_1 = n_2$, we prove that this is optimal. For cs where $n_1$ is not necessarily equal to $n_2$, we show that if there is at most one wavelength interchanger on any path from an input fiber to an output fiber, \Opt \wis are optimal. Finally, we consider a more flexible demand model where $k_1 = k_2$ but the input and output wavelengths are not specified as part of the demand. We show that $2k-1$ \wis are still necessary for any \snob \CC{k}{k}.
What Differentiates The Entrepreneurs From Non-Entrepreneurs On Nature And Nurture?

Based on the importance and contribution of entrepreneurship in economic development, it is vital to know that what underlying factors may promote the spirit of entrepreneurship? The entrepreneurship literature suggests two kinds of broader influencers or predictors for entrepreneurs and non-entrepreneurs “nature” and “nurture”. In this study “nature” includes the psychological or personality related factors; self-confidence, locus of control, risk-taking propensity and trust levels. The “nurture” is explained by the effects from society in general and friends and family in particular. To answer the question “What differentiates the entrepreneurs from non-entrepreneurs on nature and nurture? ” we collected data through questionnaire from 155 respondents. The 70 respondents were entrepreneurs and 85 were non-entrepreneurs. Step-wise discriminant analysis was used to determine the discriminating factors for entrepreneurs from non-entrepreneurs. Results indicate that societal impacts, risk taking propensity and trust levels were significantly discriminating the two groups; entrepreneurs and non-entrepreneurs. The study has important implications for policy makers, academicians, researchers and potential entrepreneurs.