Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling of framework materials at multiple scales: current practices and open questions

The last decade has seen an explosion of the family of framework materials and their study, from both the experimental and computational points of view. We propose here a short highlight of the current state of methodologies for modelling framework materials at multiple scales, putting together a brief review of new methods and recent endeavours in this area, as well as outlining some of the open challenges in this field. We will detail advances in atomistic simulation methods, the development of material databases and the growing use of machine learning for the prediction of properties. This article is part of the theme issue ‘Mineralomimesis: natural and synthetic frameworks in science and technology’.
The Potential of Dynamic Binary Modification and CPU-FPGA SoCs for Simulation

In this paper we describe a flexible infrastructure that can directly interface unmodified application executables with FPGA hardware acceleration IP in order to 1), facilitate faster computer architecture simulation, and 2), to prototype microarchitecture or accelerator IP. Dynamic binary modification tool plugins are directly interfaced to the application under evaluation via flexible software interfaces provided by a userspace hardware control library that also manages access to a parameterised Bluespec IP library. We demonstrate the potential of our infrastructure with two use cases with unmodified application executables where, 1), an executable is dynamically instrumented to generate load/store and program counter events that are sent to FPGA hardware accelerated in-order microarchitecture pipeline, and memory hierarchy models, and 2), the design of a branch predictor is prototyped using an FPGA. The key features of our infrastructure are the ability to instrument at instruction level granularity, to code exclusively at the user level, and to dynamically discover and use available hardware models at run time, thus, we enable software developers to rapidly investigate and evaluate parameterised Bluespec microarchitecture and accelerator IP models. We present a comparison between our system and GEM5, the industry standard ARM architecture simulator, to demonstrate accuracy and relative performance, even though our system is implemented on an Xilinx Zynq 7000 FPGA board with tightly coupled FPGA and ARM Cortex A9 processors, it outperforms GEM5 running on a Xeon with 32GBs of RAM (400x vs 700x slowdown over native execution).
Upregulation of the Tim-3/Galectin-9 Pathway of T Cell Exhaustion in Chronic Hepatitis B Virus Infection

The S-type lectin galectin-9 binds to the negative regulatory molecule Tim-3 on T cells and induces their apoptotic deletion or functional inactivation. We investigated whether galectin-9/Tim-3 interactions contribute to the deletion and exhaustion of the antiviral T cell response in chronic hepatitis B virus infection (CHB). We found Tim-3 to be expressed on a higher percentage of CD4 and CD8 T cells from patients with CHB than healthy controls (p<0.0001) and to be enriched on activated T cells and those infiltrating the HBV-infected liver. Direct ex vivo examination of virus-specific CD8 T cells binding HLA-A2/peptide multimers revealed that Tim-3 was more highly upregulated on HBV-specific CD8 T cells than CMV-specific CD8 T cells or the global CD8 T cell population in patients with CHB (p<0.001) or than on HBV-specific CD8 after resolution of infection. T cells expressing Tim-3 had an impaired ability to produce IFN-γ and TNF-α upon recognition of HBV-peptides and were susceptible to galectin-9-triggered cell death in vitro. Galectin-9 was detectable at increased concentrations in the sera of patients with active CHB-related liver inflammation (p = 0.02) and was strongly expressed by Kupffer cells within the liver sinusoidal network. Tim-3 blockade resulted in enhanced expansion of HBV-specific CD8 T cells able to produce cytokines and mediate cytotoxicity in vitro. Blocking PD-1 in combination with Tim-3 enhanced the number of patients from whom functional antiviral responses could be recovered and/or the strength of responses, indicating that these co-inhibitory molecules play a non-redundant role in driving T cell exhaustion in CHB. Patients taking antivirals able to potently suppress HBV viraemia continued to express Tim-3 on their T cells and respond to Tim-3 blockade. In summary, both Tim-3 and galectin-9 are increased in CHB and may contribute to the inhibition and deletion of T cells as they infiltrate the HBV-infected liver.
Interactive comment on “ Absorption , scattering and single scattering albedo of aerosols obtained from in situ measurements in the subarctic coastal region of Norway ” by E . Montilla

interpretations of the optical analysis. We would like to point out that, when we said in the manuscript that “the main goal of the campaign was to acquire a comprehensive physical and chemical characterization of local aerosol”, we didn’t mean that we had actually measured chemical properties, which we didn’t. What we mean was that we intend to infer any possible information about the composition of the particles from the measured optical data. We don’t have any chemical data measured in situ. We changed this affirmation of the manuscript, as it obviously was causing confusion and both reviewers were induced to think that we measured in situ chemical parameters.
Primary chemotherapy in surgically resectable breast cancer

We have reviewed the current status of primary chemotherapy for resectable breast cancer in view of the possibility that it may improve on results of present adjuvant drug therapies. The observed kinetic acceleration of micrometastases following noncurative surgical excision in animal studies represents strong biologic evidence supporting primary chemotherapy. From a clinical perspective, primary chemotherapy has consistently reduced the frequency of mastectomy in women with tumors initially considered too large for breast-conserving surgery. From studies of various drug combinations, it appears that the incidence of pathologic complete remission usually remains less than 10 percent. Based on results from the Milan study, it appears that the degree of tumor response is a marker of treatment outcome, at least for the first five years. A higher complete-remission rate could be expected by combining doxorubicin with paclitaxel, as has already been observed in the treatment of clinically disseminated breast cancer. In spite of the logical and scientific rationale, the available data do not as yet provide sufficient evidence to indicate a clear superiority of primary chemotherapy over adjuvant chemotherapy. The real question to answer through prospective, randomized trials is not whether the shift from adjuvant to neoadjuvant chemotherapy will result in a superior outcome, but rather how to properly integrate effective primary and adjuvant drug regimens to maximize tumor cell kill. This strategy should be further tested in patients at high risk for occult axillary adenopathy and/or distant micrometastases (i.e., tumor size larger than 2 to 3 cm). However, a more-refined risk assessment approach (e.g., using tumor grade or proliferative index) will clearly be needed. The new treatment approach may also allow for a wider use of fine-needle aspiration biopsy to obtain the primary diagnosis of cancer, a more uniform adoption of breast-conserving surgery, and use of response to chemotherapy as a marker of treatment outcome.
Demonstration of invasiveness of Vibrio parahaemolyticus in adult rabbits by immunofluorescence

To determine possible pathogenesis of Vibrio parahaemolyticus-host-organ system interactions, studies of invasiveness were made by a direct fluorescent-antibody method. Broth cultures of live cells isolated from seafish or symptomatic humans were inoculated separately into ligated ileal loops of young New Zealand white rabbits. After suitable incubation, rabbits were sacrificed, and ileal loops and tissue specimens were aseptically removed. Ileal loops were prepared and stained with specific fluorescein-tagged antibody, and organ specimens were cultured for isolation of the inoculated Vibrio strain. All strains tested penetrated into the lamina propria of the ileum and were isolated from the cultured tissue specimens, indicating that the organism is capable of more than a superficial colonization of the gut. The presence of Vibrio in cultured tissue specimens suggests invasion of deeper tissue by either the lymphatic or the circulatory system.
SYNTHETIC SEISMOGRAMS , AND SEISMIC REFLECTIONS : CORRELATIONS AT DEEP SEA DRILLING PROJECT SITE 534 , BLAKE-BAHAMA BASIN 1

Laboratory measurements on sediment samples and density well logs run at DSDP Site 534 in the Blake-Bahama Basin were used to establish an in situ velocity and density structure. Synthetic seismograms were generated for comparison to reprocessed seismic reflection data in the vicinity of the Site. Uncertainties in the relative positions of the hole and seismic reflection data, velocity corrections, and the composition of the unrecovered section were evaluated. In light of the errors and compressed section, no unique correlation of the seismic reflection data to the drill hole is completely defensible either in this chapter or elsewhere. The preferred correlation resulting from this exercise is as follows, with the Site 534 report correlation shown in parentheses where different. Horizon ß', 887 m; Horizon ß, 950 m (975 m); Horizon C , 1202 m (1250 m); Horizon C, 1268 m (1340 m); Horizon D', 1342 m (1432 m); Horizon D, 1550 m (1552 m). The major differences in these correlations arise from the use of slightly different velocities and hole location relative to the seismic profiles. The Site 534 report results rely on hole placement on a basement flank, whereas in this chapter we locate it within a basement depression still within the uncertainty of the navigation. The Site 534 report also uses drilling rates, CDP velocity analyses, sonobuoy data, and previous similar drilling correlation methods used at Site 391, along with other geologic considerations in arriving at differing results. Although the correlation method used in this investigation is more objective and the hole location uncertainties better defined, in order to have confidence in any results we will require drilling in areas where reflections are either more widely spaced or where we have better vertical velocity control in the hole.
Census from Heaven: An estimate of the global human population using night-time satellite imagery

Night-time satellite imagery provided by the Defense Meteorological Satellite Program's Operational Linescan System (DMSP OLS) is evaluated as a means of estimating the population of all the cities of the world based on their areal extent in the image. A global night-time image product was registered to a dataset of 2000 known city locations with known populations. A relationship between areal extent and city population discovered by Tobler and Nordbeck is identified on a nation by nation basis to estimate the population of the 22 920 urban clusters that exist in the night-time satellite image. The relationship between city population and city areal extent was derived from 1597 city point locations with known population that landed in a 'lit' area of the image. Due to conurbation, these 1597 cities resulted in only 1383 points of analysis for performing regression. When several cities fell into one 'lit' area their populations were summed. The results of this analysis allow for an estimate of the urban population of every nation of the world. By using the known percent of population in urban areas for every nation a total national population was also estimated. The sum of these estimates is a total estimate of the global human population, which in this case was 6.3 billion. This is fairly close to the generally accepted contemporaneous (1997) estimate of the global population which stood at approximately 5.9 billion.
Visualizing Discourse Architectures with Automatically Generated Person-Centric Social Networks

We use a person-centric network metaphor to model social environments, where each person in a conversation space is represented in terms of his or her relationships to other people based on conversation history. A network approach allows us to automatically provide users with dynamic representations of patterns within their social space and a means for navigating through them. We are currently developing two sample applications: one based on a user’s email behavior that creates a dynamic interface representing the user’s personal social network (Personal Map); and another based on distribution list memberships that provides a map of the connections between researchers at MSR (MSR Connections). Our goal is to enhance the user’s ability to seek out social information and manage online social relationships.
Output-Driven Distributed Optimistic Message Logging and Checkpointing

Although optimistic fault tolerance methods using message logging and checkpointing have the potential to provide highly e cient transparent fault tolerance in distributed systems existing methods are limited by several factors Coordinating the asynchronous message logging progress among all processes of the system may cause signi cant over head limiting their ability to scale to large systems and o setting some of the per formance gains over simpler pessimistic methods Furthermore logging all messages received by each process may place a substantial load on the network and le server in systems with high communication rates Finally existing methods do not support nondeterministic process execution such as occurs in multithreaded processes and those that handle asynchronous interrupts This paper presents a new method using optimistic message logging and checkpointing that addresses these limitations Any fault tolerance method must delay output from the system to the outside world until it can guarantee that no future failure can force the system to roll back to a state before the output was sent With this new method only this need to commit output forces any process to log received messages or to checkpoint Each process commits its own output with the cooperation of the minimum number of other processes and any messages not needed to allow pending output to be committed need not be logged Individual processes may also dynamically switch to checkpointing without message logging to avoid the expense of logging a large number of messages or to support their own nondeterministic execution
Deletions in chromosome arms 3p and 11q are new prognostic markers in localized and 4s neuroblastoma.

PURPOSE To find new nonrandom chromosomal changes in neuroblastoma (NB) with a potential to forecast the patient's outcome, alterations in chromosome arms 3p and 11q were investigated. EXPERIMENTAL DESIGN Frequency and prognostic potential of 3p and 11q alterations in 144 NBs were analyzed using interphase fluorescence in situ hybridization with DNA probes for 3p26 and 11q23. Aberrations were defined as deletion (monosomy of a specific region) or imbalance (at least two intact and additional 3p26- or 11q23-deleted chromosomes). RESULTS Forty-two of 144 cases (29%) displayed 11q alterations (21% deletions, 8% imbalances). Most aberrations were associated with stage 4 disease (28 of 59, 47%) but were also present in localized and 4s tumors (14 of 85, 16%; P = 0.007). Patients with 11q deletion/imbalance were significantly older at diagnosis (P < 0.001). Changes in 3p were detected in 26 of 144 (18%) samples (15% deletions, 3% imbalances). These alterations were also associated with stage 4 [20 of 59 (34%) versus 6 of 85 (7%) in stages 1-3 and 4s, P = 0.007], and the median age was increased (P < 0.001). Aberrations in both chromosomes were highly associated with each other (P < 0.001). MYCN amplification (MNA) was detected in 10% and 12% of tumors with 11q and 3p alterations, and changes in 1p36 occurred in 13% and 26% of the 3p- and 11q-aberrant tumors. MYCN amplification and 11q deletion/imbalance tended to show an inverse correlation (P = 0.07) as well as 1p and 3p deletion/imbalance (P = 0.07). Patients with 3p and 11q abnormalities in localized/4s tumors showed an inferior outcome compared with those without these alterations (P = 0.002 and P = 0.0027, respectively), in particular in MYCN single copy tumors (P < 0.0001 and P = 0.0006, respectively). CONCLUSION Alterations in 3p and 11q are frequent nonrandom aberrations in NB and define a new high-risk subgroup in MYCN single copy stage 1-3 and 4s disease.
Fibred Coalgebraic Logic and Quantum Protocols

Motivated by applications in modelling quantum systems using coalgebraic techniques, we introduce a fibred coalgebraic logic. Our approach extends the conventional predicate lifting semantics with additional modalities relating conditions on different fibres. As this fibred setting will typically involve multiple signature functors, the logic incorporates a calculus of modalities enabling the construction of new modalities using various composition operations. We extend the semantics of coalgebraic logic to this setting, and prove that this extension respects behavioural equivalence. We show how properties of the semantics of modalities are preserved under composition operations, and then apply the calculational aspect of our logic to produce an expressive set of modalities for reasoning about quantum systems, building these modalities up from simpler components. We then demonstrate how these modalities can describe some standard quantum protocols. The novel features of our logic are shown to allow for a uniform description of unitary evolution, and support local reasoning such as "Alice's qubit satisfies condition" as is common when discussing quantum protocols.
Topoisomerase I and II Inhibitors: A Patent Review.

BACKGROUND Topoisomerases are a set of nuclear enzymes that play a vital role in handling of topological consequences of DNA during various genetic activities necessary for vitality of cell. Inhibition of these enzymes consequently leads to the blockage of ligation step of the cell cycle which generates single and double strand breakage in DNA strand. Introduction of these breaks subsequently leads to programmed cell death (Apoptosis). OBJECTIVE In the past several years, topoisomerases have become one of the most expedient and strategic molecular targets for anticancer drugs and numerous patents have been filed and published on topoisomerase inhibitors. This review compiles the patent literature up to 2016 embracing topo I and II inhibitors as well as dual inhibitors which are structurally adjacent to camptothecin (CPT), natural products such as lamellarins and synthetic trisubstituted pyridines. The present assemblage can be extremely advantageous for the medicinal chemists who are in crave for the development of potential anticancer agents targeting topoisomerases. CONCLUSION Recent patents indicated that some of the nitrogen containing heteroaromatic compounds have immense potential to inhibit topoisomerase enzyme. In particular, fused N-Heterocycles can be anticipated for their promising therapeutic potential alone or in combination with other anticancer agents. Naphthyridinone and indenoisoquinoline derivatives, described in the preceding sections of this review, are endowed with significant potency against topoisomerase I which clearly indicates the need of preclinical and clinical studies to place them in forefront as potential future drug candidates.
Clustered Pathway Genes in Aflatoxin Biosynthesis

Aflatoxins, a group of polyketide-derived furanocoumarins (Fig. [1][1]), are the most toxic and carcinogenic compounds among the known mycotoxins. Among the at least 16 structurally related aflatoxins characterized, however, there are only four major aflatoxins, B1, B2, G1, and G2 (AFB1, AFG1, AFB2
Inductive power transfer apparatus and electric autocycle charger including same

The invention provides an inductive power transfer apparatus and an electric autocycle charger including the same. The embodiment provides an electric autocycle support apparatus comprising an autocycle engagement device adapted to support an autocycle, the engagement device having a coil adapted to provide a magnetic field for inductively charging an autocycle supported by the apparatus. The invention also provides an electric autocycle stand and a charging system.
Quantification of maternal microchimerism by HLA-specific real-time polymerase chain reaction: studies of healthy women and women with scleroderma.

OBJECTIVE Microchimerism (Mc), originating from bidirectional fetal-maternal cell traffic during pregnancy, has recently been identified in healthy adults and in patients with scleroderma (systemic sclerosis [SSc]). This study was undertaken to investigate the frequency and quantitative levels of maternal Mc (MMc) in healthy women and women with SSc. METHODS HLA-specific primers and fluorogenic probes were used in real-time quantitative polymerase chain reaction assays to detect and quantify MMc by targeting noninherited, nonshared HLA sequences. DNA-based HLA typing was conducted in 67 proband-mother pairs and in all children if the proband was parous. Statistical analysis was limited to 50 proband-mother pairs (including 32 healthy women and 18 women with SSc) in whom MMc could be distinguished from potential fetal Mc. RESULTS MMc in peripheral blood mononuclear cells was more frequent among women with SSc (72%) than healthy women (22%) (odds ratio 9.3, P = 0.001). However, levels of MMc, expressed as the genome equivalent of maternal cells per million (gEq/mil), were not significantly different (0-68.6 gEq/mil in SSc patients, 0-54.5 in healthy women). In additional studies, positivity for MMc was demonstrated in a bone marrow aspirate from an SSc patient in whom peripheral blood had been found to be negative for MMc on 4 occasions, and tissue from a subsequent autopsy of this patient had MMc levels of 757 and 1,489 gEq/mil in the lung and heart, respectively. CONCLUSION MMc is not uncommon in the peripheral blood of healthy adults, is increased in frequency in patients with SSc, and may be present in bone marrow and disease-affected tissues although absent in the peripheral blood.
An Inquiry into the Utilization of Behavior of Users in Personalized Web

Nowadays we see successive transformation of the Web into its personalized form. In order to personalize the content to suit each user's requirements we need to acquire the user's interests. Utilization of implicit feedback is the most suitable and unobtrusive way of doing so. In this paper we present various forms of implicit feedback and their application in the estimation of user's interests. We propose a method of link recommendation based on the recorded actions users take while visiting a website. We employ collaborative filtering to predict user interest to unvisited pages. We present an evaluation of our method using the web portal of our faculty where personalized recommendation of links to interesting events is provided for visitors.