Miracle-dz/UniFAR-FTUs huggingface dataset:
A Lightweight Approach to Manifesting Responsible Parties for TCP Packet Loss

—Troubleshooting TCP packet loss is a crucial problem for many network applications. TCP packets could be lost in different network segments for various reasons. Understanding the responsible parties for TCP loss is an important step for network operators to diagnose related problem. However, TCP is designed for end-to-end control. It is difﬁcult for any third party to detect whether and where (even coarsely) TCP packet loss has occurred. We design TCPBisector , a lightweight efﬁcient diagnosis tool to manifest responsible parties for TCP packet loss. TCPBisector divides the responsibility between “My” and “Other” parties or networks (denoted as Net m and Net o ) conceptually delimited by a passive network measurement point (denoted as MP), and quantiﬁes the responsibility by using TCP packet loss ratios on the corresponding networks. The evaluation shows that the TCPBisector can accurately estimate TCP packet loss ratios with estimation error rate 3.5-6.9%.
Multi-objective Layout Optimization for Branch Pipe of Aero-engine Based on MOPSO

： The layout optimization of branch pipe is a NP hard problem, and the multi-objective case of which is more complex. The branch pipe routing problem is studied in the context of an aero-engine development, and a model of multi-objective routing for branch pipes is constructed based on Steiner tree, where pipe length, the number of branch points and pipeline smoothness are taken into consideration as optimal objectives. Considering the complexity of the problem, a multi-objective particle swarm optimization (MOPSO)-based layout method is designed to solve the constructed routing model. More specifically, the number and coordinates of branch points are selected as decision variables; according to the characteristic topological structure of branch pipes, a computation model of smoothness is presented, and the multi-objective evaluation is then completed by non-dominated sorting and grid density calculation; in addition, the visibility graph method and geodesic are integrated to handle routing constraints; The Pareto solution set is obtained through particle evolution. The presented routing model and method consider the cases of multiple pipe terminals, multi-objectives and obstacle-avoidance constraints. Finally, the feasibility of the proposed method is demonstrated by several numerical computations of branch pipe routing examples.
Inhibition of Escherichia coli CFT073 ﬂiC Expression and Motility by Cranberry Materials (cid:1)

In humans, uropathogenic Escherichia coli (UPEC) is the most common etiological agent of uncomplicated urinary tract infections (UTIs). Cranberry extracts have been linked to the prevention of UTIs for over a century; however, a mechanistic understanding of the way in which cranberry derivatives prevent bacterial infection is still lacking. In this study, we used a ﬂiC-lux reporter as well as quantitative reverse transcription-PCR to demonstrate that when UPEC strain CFT073 was grown or exposed to dehydrated, crushed cranberries or to puriﬁed cranberry-derived proanthocyanidins (cPACs), expression of the ﬂagellin gene ( ﬂiC ) was inhib-ited. In agreement with these results, transmission electron microscopy imaging of bacteria grown in the presence of cranberry materials revealed fewer ﬂagella than those in bacteria grown under control conditions. Furthermore, we showed that swimming and swarming motilities were hindered when bacteria were grown in the presence of the cranberry compounds. Because ﬂagellum-mediated motility has been suggested to enable UPEC to disseminate to the upper urinary tract, we propose that inhibition of ﬂagellum-mediated motility might be a key mechanism by which cPACs prevent UTIs. This is the ﬁrst report to show that cranberry compounds inhibit UPEC motility via downregulation of the ﬂiC gene. Further studies are required to establish whether these inhibitors play a role in vivo .
On the Hölder continuity of ring Q-homeomorphisms

Abstract We prove the Hölder continuity of a homeomorphism f defined on a bounded domain Ω ⊂ ℝ n {\Omega\subset\mathbb{R}^{n}} with Lipschitz boundary. The homeomorphism f is assumed to belong to a certain Orlicz–Sobolev class and to satisfy a distortion condition near the boundary.
Dichotomous role of autophagy in cancer

Abstract Autophagy is an evolutionary conserved catabolic process that plays physiological and pathological roles in a cell. Its effect on cellular metabolism, the proteome, and the number and quality of organelles, diversely holds the potential to alter cellular functions. It acts paradoxically in cancer as a tumor inhibitor as well as a tumor promoter. In the early stage of tumorigenesis, it prevents tumor initiation by the so-called “quality control mechanism” and suppresses cancer progression. For late-staged tumors that are exposed to stress, it acts as a vibrant process of degradation and recycling that promotes cancer by facilitating metastasis. Despite this dichotomy, the crucial role of autophagy is evident in cancer, and associated with mammalian targets of rapamycin (mTOR), p53, and Ras-derived major cancer networks. Irrespective of the controversy regarding autophagic manipulation, promotion and suppression of autophagy act as potential therapeutic targets in cancer treatment and may provide various anticancer therapies.
Institutional Knowledge at Singapore Management University Institutional Knowledge at Singapore Management University Specification test for spatial autoregressive models Specification test for spatial autoregressive models

This article considers a simple test for the correct speciﬁcation of linear spatial autoregressive models, assuming that the choice of the weight matrix W n is true. We derive the limiting distributions of the test under the null hypothesis of correct speciﬁcation and a sequence of local alternatives. We show that the test is free of nuisance parameters asymptotically under the null and prove the consistency of our test. To improve the ﬁnite sample performance of our test, we also propose a residual-based wild bootstrap and justify its asymptotic validity. We conduct a small set of Monte Carlo simulations to investigate the ﬁnite sample properties of our tests. Finally, we apply the test to two empirical datasets: the vote cast and the economic growth rate. We reject the linear spatial autoregressive model in the vote cast example but fail to reject it in the economic growth rate example. Supplementary materials for this article are available online.
Edinburgh Research Explorer Fogarty International Center collaborative networks in infectious disease modeling

infectious disease threats. The Multinational Influenza Seasonal Mortality Study (MISMS) has strengthened global capacity to study the epidemiology and evolutionary dynamics of influenza viruses in 80 countries by organizing inter- national research activities and training workshops. The Research and Policy in Infectious Disease Dynamics (RAPIDD) program and its precursor activities has established a network of global experts in infectious disease modeling operating at the research-policy interface, with collaborators in 78 countries. These activities have provided evidence-based recommendations for disease control, including during large-scale outbreaks of pan- demic influenza, Ebola and Zika virus. Together, these programs have coordinated international collaborative networks to advance the study of emerging disease threats and the field of computational epidemic modeling. A global community of researchers and policy-makers have used the tools and trainings developed by these programs to interpret infectious disease patterns in their countries, understand modeling concepts, and inform control policies. Here we reflect on the scientific achievements and lessons learnt from these programs (h-index=106 for RAPIDD and 79 for MISMS), including the identification of outstanding researchers and fellows; funding flexibility for timely research workshops and working groups (particularly relative to more traditional investigator-based grant programs); emphasis on group activities such as large-scale modeling reviews, model comparisons, forecasting challenges and special journal issues; strong quality control with a light touch on outputs; and prominence of training, data-sharing, and joint publications.
COMPARATIVE STUDY OF MICROSCOPY WITH ELISA ANTIBODY BASED AMOEBIASIS DIAGNOSIS IN PATIENTS PRESENTING WITH DYSENTERY AT GOVERNMENT HOSPITALS IN KADUNA

This study investigated the prevalence and risk factors of Entamoeba histolytica infection among dysentery patients presenting at government hospitals in Kaduna metropolis. Three hundred and seventy eight (378) samples were collected, comprising 189 stool and 189 serum specimens. The stool and serum specimens were analysed using Microscopy and Enzyme Linked Immunosorbent Assay (ELISA) respectively. Of the 189 patients sampled, 27 (14.3%) were positive for Entamoeba histolytica , 13 (6.9%) Entamoeba coli and 4 (2.1%) Giardia lamblia . The prevalence of E. histolytica infection (14.3%) was higher than the 10% recorded by WHO (1995) in the developing world. Individuals in the age group 1-10 years had the highest prevalence (29.40%) and it decreased with age except for age group 41 years and above. Males were more infected (14.6%) than females (14.0%) but the difference was not statistically significant (p > 0.05). The infection rate was higher in the rainy season (15.5%) than the dry season (12.9%). The study also revealed that E. histolytica infection was not statistically associated with educational status and type of toilet facility (p > 0.05), but it was however, statistically associated with the occupational status and source of drinking water of the patients (p < 0.05). include the socio-economic population expertise of the researchers, subjects enrolled in the study and the duration of the
Positive association of serum FUT8 activity with renal tubulointerstitial injury in IgA nephropathy patients

α‐1,6 Fucosyltransferase (FUT8) appears to play an essential role in the pathogenesis of renal fibrosis. However, it remained unknown whether FUT8 also contributed to renal fibrosis in immunoglobulin A nephropathy (IgAN). In the present study, we explored the association of serum FUT8 activity with renal tubulointerstitial injury in IgAN patients.
Toolbox for reconstructing quantum theory from rules on information acquisition

We develop an operational approach for reconstructing the quantum theory of qubit systems from elementary rules on information acquisition. The focus lies on an observer O interrogating a system S with binary questions and S's state is taken as O's `catalogue of knowledge' about S. The mathematical tools of the framework are simple and we attempt to highlight all underlying assumptions. Four rules are imposed, asserting (1) a limit on the amount of information available to O; (2) the mere existence of complementary information; (3) O's total amount of information to be preserved in-between interrogations; and, (4) O's `catalogue of knowledge' to change continuously in time in-between interrogations and every consistent such evolution to be possible. This approach permits a constructive derivation of quantum theory, elucidating how the ensuing independence, complementarity and compatibility structure of O's questions matches that of projective measurements in quantum theory, how entanglement and monogamy of entanglement, non-locality and, more generally, how the correlation structure of arbitrarily many qubits and rebits arises. The rules yield a reversible time evolution and a quadratic measure, quantifying O's information about S. Finally, it is shown that the four rules admit two solutions for the simplest case of a single elementary system: the Bloch ball and disc as state spaces for a qubit and rebit, respectively, together with their symmetries as time evolution groups. The reconstruction for arbitrarily many qubits is completed in a companion paper (arXiv:1511.01130) where an additional rule eliminates the rebit case. This approach is inspired by (but does not rely on) the relational interpretation and yields a novel formulation of quantum theory in terms of questions.
Changes in seam number and location induce holes within microtubules assembled from porcine brain tubulin and in Xenopus egg cytoplasmic extracts

Microtubules are tubes of about 25 nm in diameter that are critically involved in a variety of cellular functions including motility, compartmentalization, and division. They are considered as pseudo-helical polymers whose constituent αβ-tubulin heterodimers share lateral homotypic interactions, except at one unique region called the seam. Here, we used a segmented sub-tomogram averaging strategy to reassess this paradigm and analyze the organization of the αβ-tubulin heterodimers in microtubules assembled from purified porcine brain tubulin in the presence of GTP and GMPCPP, and in Xenopus egg cytoplasmic extracts. We find that in all conditions, microtubules incorporate variable protofilament and/or tubulin subunit helical-start numbers, as well as variable numbers of seams. Strikingly, the seam number and location vary along individual microtubules, generating holes of one to a few subunits in size within their lattices. Together, our results reveal that the formation of mixed and discontinuous microtubule lattices is an intrinsic property of tubulin that requires the formation of unique lateral interactions without longitudinal ones. They further suggest that microtubule assembly is tightly regulated in a cytoplasmic environment.
MND1 and PSMC3IP control PARP inhibitor sensitivity in mitotic cells

The PSMC3IP-MND1 heterodimer promotes RAD51 and DMC1-dependent D-loop formation during meiosis in yeast and mammalian organisms. For this purpose, it catalyzes the DNA strand exchange activities of the recombinases. Interestingly, in a panel of genome-scale CRISPR-Cas9 mutagenesis and interference screens in mitotic cells, we found that depletion of either PSMC3IP or MND1 caused sensitivity to clinical Poly (ADP-Ribose) Polymerase inhibitors (PARPi). A retroviral mutagenesis screen in mitotic cells also identified PSMC3IP and MND1 as genetic determinants of ionizing radiation sensitivity. The role PSMC3IP and MND1 play in preventing PARPi sensitivity in mitotic cells appears to be independent of a previously described role in alternative lengthening of telomeres (ALT). PSMC3IP or MND1 depleted cells accumulate toxic RAD51 foci in response to DNA damage, show impaired homology-directed DNA repair, and become PARPi sensitive, even in cells lacking both BRCA1 and TP53BP1. Although replication fork reversal is also affected, the epistatic relationship between PSMC3IP-MND1 and BRCA1/BRCA2 suggests that the abrogated D-loop formation is the major cause of PARPi sensitivity. This is corroborated by the fact that a PSMC3IP p.Glu201del D-loop formation mutant associated with ovarian dysgenesis fails to reverse PARPi sensitivity. These observations suggest that meiotic proteins such as MND1 and PSMC3IP could have a greater role in mitotic cells in determining the response to therapeutic DNA damage.
Coupling of metataxonomics and culturing improves bacterial diversity characterization and identifies a novel Rhizorhapis sp. with metal resistance potential in a multi-contaminated waste sediment

Long-term contaminated environments have been recognized as potential hotspots for bacterial discovery in taxonomic and functional terms for bioremediation purposes. Here, bacterial diversity in waste sediment collected from a former industrial dumpsite and contaminated with petroleum hydrocarbon and heavy metals was investigated through the parallel application of culture-independent (16S rRNA gene amplicon sequencing) and -dependent (plate culturing followed by colony picking and identification of isolates by 16S rRNA gene Sanger sequencing) approaches. The bacterial diversities retrieved by both approaches greatly differed. Bacteroidetes and Proteobacteria were dominant in the culture-independent community, while Firmicutes and Actinobacteria were the main culturable groups. Only 2.7% of OTUs (operational taxonomic units) in the culture-independent dataset were cultured. Most of the culturable OTUs were absent or in very low abundances in the culture-independent dataset, revealing that culturing is a useful tool to study the rare bacterial biosphere. One culturable OTUs (comprising only the isolate SPR117) was identified as a potential new species in the genus Rhizorhapis (class Alphaproteobacteria) and was selected for further characterization. Phytopathogenicity tests showed that Rhizorhapis sp. strain SPR117 (ATCC TSD-228) is not pathogenic for lettuce, despite the only described species within this genus, Rhizorhapis suberifaciens, is causal agent of the lettuce corky root disease. The genome of the strain SPR117 was sequenced, assembled in 256 contigs, with a length of 4,419,522 bp and a GC content of 59.9%), and its further annotation revealed the presence of genes related to the resistance to arsenic, copper, iron, and mercury, among other metals. Therefore, the coupling of metataxonomics and culturing is a useful tool to obtain not only an improved description of bacterial communities in contaminated environments, but also to isolate microorganisms with bioremediation potential.
Sensitivity to naturalistic texture relies primarily on high spatial frequencies

Natural images contain information at multiple spatial scales. Although we understand how early visual mechanisms split multi-scale images into distinct spatial frequency channels, we do not know how the outputs of these channels are processed further by mid-level visual mechanisms. We have recently developed a naturalness discrimination task that uses synthesized, multi-scale textures to isolate these mid-level mechanisms (Freeman et. al. 2013). Here, we use three experimental manipulations (image blur, image rescaling, and eccentric viewing) to show that naturalness sensitivity is strongly dependent on image features at high object spatial frequencies (measured in cycles/image). As a result, sensitivity depends on a texture acuity limit, a property of the visual system that sets the highest retinal spatial frequency (measured in cycles/degree) that can be used to solve the task. A model observer analysis shows that high object spatial frequencies carry more task-relevant information than low object spatial frequencies. Comparing the outcome of this analysis with human performance reveals that human observers’ efficiency is similar for all object spatial frequencies. We conclude that the mid-level mechanisms that underlie naturalness sensitivity effectively extract information from all image features below the texture acuity limit, regardless of their retinal and object spatial frequency.
Decades of Trivers-Willard research on humans: what conclusions can be drawn?

The Trivers-Willard hypothesis predicts that parents in good condition are positively biased towards sons, while parents in poor condition are positively biased towards daughters. An extensive literature testing this hypothesis has accumulated in the last five decades. We take stock of results concerning humans in a systematic review, which yielded 87 articles, reporting a total of 821 hypothesis tests. A p-curving analysis did not reveal a pattern of p-values consistent with p-hacking. Effects are consistent with the Trivers-Willard hypothesis overall. We then went on to check whether there was a difference between sex ratio and post-birth investment. Theoretical work suggests that, the conditions under which the Trivers-Willard hypothesis is verified should be more restrictive in the case of post-birth investment than for sex ratio. We explored this question in two ways and obtained mixed results. We put forward recommendations for future studies that aim to further assess the validity of the Trivers-Willard hypothesis or mechanisms subtending it, and we discuss the implications of different ways of measuring parental status and investment.
Combined in vivo and in situ genome-resolved metagenomics reveals novel symbiotic

25 Non-cyanobacteria diazotrophs (NCDs) were shown to dominate in surface waters shifting the 26 long-held paradigm of cyanobacteria dominance and raising fundamental questions on how 27 these putative heterotrophic bacteria thrive in sunlit oceans. Here, we report an unprecedented 28 finding in the widely used model diatom Phaeodactylum tricornutum ( Pt ) of NCDs sustaining 29 diatom cells in the absence of bioavailable nitrogen. We identified Pt NCDs using 30 metagenomics sequencing and detected nitrogenase gene in silico and/or by PCR. We 31 demonstrated nitrogen fixation in Pt NCDs and their close genetic affiliation with NCDs from 32 the environment. We showed the wide occurrence of this type of symbiosis with the isolation 33 of NCDs from other microalgae, their identification in the environment, and predicted their 34 associations with photosynthetic microalgae. Overall, this study provides evidence for a 35 previously overlooked symbiosis using a multidisciplinary model-based approach, which will 36 help understand the different players driving global marine nitrogen fixation.
Through the eye to the brain: Modulating LC-mediated arousal via pupil-based neurofeedback

The brain’s state of arousal influences cognitive functioning and mental well-being. It is controlled by several neuromodulatory nuclei in the brainstem and, particularly, by the locus coeruleus (LC). The LC is the main source of noradrenaline (NA) in the central nervous system where it exerts powerful effects on neural processing and autonomic function. Here, we investigate whether human participants can gain volitional control of their brain’s arousal state using a new neurofeedback approach which exploits the mechanism that the eye’s pupil diameter provides an indirect readout of arousal if light conditions are controlled. We show that pupil-based neurofeedback training is essential for learning how to self-regulate pupil size. Once acquired, pupil self-regulation significantly modulates neuromodulatory brainstem centers involved in arousal control and particularly the LC-NA system when carefully measured with functional magnetic resonance imaging. Further, it modulates heart rate, a cardiovascular marker of autonomic function, and it has a significant effect on behavior and specific psychophysiological responses during an oddball task, an attention task that has been shown to be evoke stimulus-dependent LC-NA activity. Considering the modulatory effects of the LC-NA system and other arousal-regulating centers on cognitive functioning and various behaviors including stress-related responses, pupil-based neurofeedback has a tremendous potential to be translated to behavioral and clinical applications across various domains.