Miracle-dz/UniFAR-FTUs huggingface dataset:
Davydov-Type Excitonic Eﬀects on the Absorption Spectra of Parallel-Stacked and Herringbone Aggregates of Pentacene: Time-Dependent Density-Functional Theory and Time-Dependent Density-Functional Tight Binding

Exciton formation leads to J-bands in solid pentacene. Describing these exciton bands represents a challenge for both time-dependent (TD) density-functional theory (DFT) and for its semi-empirical analogue, namely for TD density-functional tight binding (DFTB) for three reasons: (i) solid pen-tacene and pentacene aggregates are bound only by van der Waals forces which are notoriously diﬃcult to describe with DFT and DFTB, (ii) the proper description of the long-range coupling between molecules, needed to describe Davydov splitting, is not easy to include in TD-DFT with traditional functionals and in TD-DFTB, and (iii) mixing may occur between local and charge transfer excitons, which may, in turn, require special functionals. We assess how far TD-DFTB has progressed towards a correct description of this type of exciton by including both a dispersion correction for the ground state and a range-separated hybrid functional for the excited state and comparing the results against corresponding TD-CAM-B3LYP/CAM-B3LYP+D3 results. Analytic results for parallel-stacked ethylene are derived which go beyond Kasha’s exciton model [Kasha, Rawls, and El-Bayoumi, Pure Appl. Chem. 11 , 371 (1965)] in that we are able to make a clear distinction between charge transfer and energy transfer excitons. This is further conﬁrmed when it is shown that range-separated hybrids have a markedly greater eﬀect on charge-transfer excitons than on energy-transfer excitons in the case of parallel-stacked pentacenes. TD-DFT calculations with the CAM-B3LYP functional and TD-lc-DFT calculations lead to negligeable excitonic corrections for the herringbone crystal structure, possibly because of an overcorrection of charge-transfer eﬀects. In this case, TD-DFT calculations with the B3LYP functional or TD-DFTB calculations parameterized to B3LYP give the best results for excitonic corrections for the herringbone crystal structure as judged from comparison with experimental spectra and with Bethe-Salpeter equation calculations from the literature.
Cell‐Cycle Arrest at G2/M and Growth Inhibition by Apigenin in Human Colon Carcinoma Cell Lines

Apigenin, a common dietary flavonoid, has been shown to induce cell cycle arrest in both epidermal and fibroblast cells and inhibit skin tumorigenesis in murine models. The present study assessed the influence of apigenin on cell growth and the cell cycle in the human colon carcinoma cell lines SW480, HT‐29, and Caco‐2. Treatment of each cell line with apigenin (0–80 μM) resulted in a dose‐dependent reduction in both cell number and cellular protein content, compared with untreated control cultures. DNA flow cytometric analysis indicated that treatment with apigenin resulted in G2/M arrest in all three cell lines in a time‐ and dose‐dependent manner. Apigenin treatment (80 μM) for 48 h produced maximum G2/M arrest of 64%, 42%, and 26% in SW480 cells, HT‐29 cells, and Caco‐2 cells, respectively, in comparison with control cells (15%). The proportion of S‐phase cells was not altered by apigenin treatment in each of the three cell lines. The G2/M arrest was reversible after 48 h of apigenin treatment in the most sensitive cell line SW480. The degree of G2/M arrest by apigenin was inversely correlated with the corresponding inhibition of cell growth measurements in all three cell lines (r = −0.626 to −0.917, P≤0.005). Moreover, an immune complex kinase assay demonstrated an inhibition of p34cdc2 kinase activity, a critical enzyme in G2/M transition, in each cell line after treatment with apigenin (50–80 μM). Western blot analyses indicated that both p34cdc2 and cyclin B1 proteins were also decreased after apigenin treatment. These results indicate that apigenin inhibits colon carcinoma cell growth by inducing a reversible G2/M arrest and that this arrest is associated, at least in part, with inhibited activity of p34cdc2 kinase and reduced accumulation of p34cdc2 and cyclin B1 proteins. Differences in induction of G2/M arrest by apigenin in the three colon carcinoma cell lines suggest that dietary apigenin may be differentially effective against tumors with specific mutational spectra. Mol. Carcinog. 28:102–110, 2000. © 2000 Wiley‐Liss, Inc.
Bayesian Modeling and Chronological Precision for Polynesian Settlement of Tonga

First settlement of Polynesia, and population expansion throughout the ancestral Polynesian homeland are foundation events for global history. A precise chronology is paramount to informed archaeological interpretation of these events and their consequences. Recently applied chronometric hygiene protocols excluding radiocarbon dates on wood charcoal without species identification all but eliminates this chronology as it has been built for the Kingdom of Tonga, the initial islands to be settled in Polynesia. In this paper we re-examine and redevelop this chronology through application of Bayesian models to the questioned suite of radiocarbon dates, but also incorporating short-lived wood charcoal dates from archived samples and high precision U/Th dates on coral artifacts. These models provide generation level precision allowing us to track population migration from first Lapita occupation on the island of Tongatapu through Tonga’s central and northern island groups. They further illustrate an exceptionally short duration for the initial colonizing Lapita phase and a somewhat abrupt transition to ancestral Polynesian society as it is currently defined.
Direct observation of the thermal demagnetization of magnetic vortex structures in nonideal magnetite recorders

The thermal demagnetization of pseudo‐single‐domain (PSD) magnetite (Fe3O4) particles, which govern the magnetic signal in many igneous rocks, is examined using off‐axis electron holography. Visualization of a vortex structure held by an individual Fe3O4 particle (~250 nm in diameter) during in situ heating is achieved through the construction and examination of magnetic‐induction maps. Stepwise demagnetization of the remanence‐induced Fe3O4 particle upon heating to above the Curie temperature, performed in a similar fashion to bulk thermal demagnetization measurements, revealed that its vortex state remains stable under heating close to its unblocking temperature and is recovered upon cooling with the same or reversed vorticity. Hence, the PSD Fe3O4 particle exhibits thermomagnetic behavior comparable to a single‐domain carrier, and thus, vortex states are considered reliable magnetic recorders for paleomagnetic investigations.
Text-Image Transformer with Cross-Attention for Visual Question Answering

Visual question answering (VQA) is a challenging task that requires multimodal reasoning and knowledge. In this study, we explored different methods of feature fusion for VQA, using pre-trained models to encode the text and image features, and then applying different attention mechanisms to fuse them. We evaluated our methods on the DAQUAR dataset. We used three metrics to measure the performance of our methods: WUPS, Acc, and F1. We found that concatenating raw text and image features performs slightly better than self-attention for VQA. We also found that using text as query and image as key and value performs worse than other methods of cross-attention or self-attention for VQA, because it might not capture the bidirectional interactions between the text and image modalities. We discussed possible explanations and examples for these findings.
Cooperative Logistics: Can Artiﬁcial Intelligence Enable Trustworthy Cooperation at Scale?

Cooperative Logistics studies the setting where logistics companies pool their resources together to improve their individual performance. Prior literature suggests carbon savings of approximately 22%. If attained globally, this equates to 480,000,000 tonnes of CO 2 . Whilst well-studied in operations research – industrial adoption remains limited due to a lack of trustworthy cooperation. A key remaining challenge is fair and scalable gain sharing (i.e., how much should each company be fairly paid? ). This paper introduces the novel algorithmic challenges that Cooperative Logistics offers AI, and novel applications of AI towards Cooperative Logistics. We further present ﬁndings from our initial experiments.
The association between persistent organic pollutants, type 2 diabetes, and insulin resistance in two First Nations communities in Northen Ontario

Recent evidence suggests an association between persistent organic pollutants (POPs) and type 2 diabetes. In two First Nations communities of high wild food consumption, specific objectives were formulated to: 1) compare POP levels between diabetics and non-diabetics; 2) investigate the association between POPs and insulin resistance in non-diabetics; and 3) determine the effects of POPs on certain inflammatory markers. Results indicated significantly higher age-adjusted plasma concentrations of some POPs in diabetics as compared to non-diabetics. Body mass index was found to be the most significant predictor of insulin resistance. There was a positive association of Tumour Necrosis Factor (TNF)-a with oxychlordane and mono/di-ortho substituted polychlorinated biphenyls (PCBs). Positive associations were detected between adiponectin and mono/di-ortho substituted PCBs as well as some pesticides. Results indicate that diabetics have higher levels of some POPs than non-diabetics. In nondiabetics, POPs are unrelated to insulin resistance although some are positively associated with inflammatory markers.
A unified CSF-based framework for edge detection and edge visibility

One important trend in edge detection starts from current knowledge about the Human Visual System (HVS) in order to mimic some of its components. We follow this trend and propose a new edge detector which also computes the edge visibility for the HVS. Two important processes in the HVS are taken into account: visual adaptation and contrast sensitivity. Our model is in good agreement with some classical results in human vision, such as Weber's law and Ricco's law, as well as the visibility of sine and square gratings. The main contribution is to propose a unified framework, biologically inspired, which mimics human vision and computes both edge localization and edge visibility. Compared to previous approaches, the visibility of a target is estimated without segmentation of the target. This work may contribute to military applications, Intelligent Transportation Systems, and low vision simulation.
Spectral Entropy as an Electroencephalographic Measure of Anesthetic Drug Effect: A Comparison with Bispectral Index and Processed Midlatency Auditory Evoked Response

Background:The authors compared the behavior of two calculations of electroencephalographic spectral entropy, state entropy (SE) and response entropy (RE), with the A-Line® ARX Index (AAI) and the Bispectral Index (BIS) and as measures of anesthetic drug effect. They compared the measures for baseline variability, burst suppression, and prediction probability. They also developed pharmacodynamic models relating SE, RE, AAI, and BIS to the calculated propofol effect-site concentration (Ceprop). Methods:With institutional review board approval, the authors studied 10 patients. All patients received 50 mg/min propofol until either burst suppression greater than 80% or mean arterial pressure less than 50 mmHg was observed. SE, RE, AAI, and BIS were continuously recorded. Ceprop was calculated from the propofol infusion profile. Baseline variability, prediction of burst suppression, prediction probability, and Spearman rank correlation were calculated for SE, RE, AAI, and BIS. The relations between Ceprop and the electroencephalographic measures of drug effect were estimated using nonlinear mixed effect modeling. Results:Baseline variability was lowest when using SE and RE. Burst suppression was most accurately detected by spectral entropy. Prediction probability and individualized Spearman rank correlation were highest for BIS and lowest for SE. Nonlinear mixed effect modeling generated reasonable models relating all four measures to Ceprop. Conclusions:Compared with BIS and AAI, both SE and RE seem to be useful electroencephalographic measures of anesthetic drug effect, with low baseline variability and accurate burst suppression prediction. The ability of the measures to predict Ceprop was best for BIS.
Immunogenicity and protection against genital Chlamydia infection and its complications by a multisubunit candidate vaccine.

BACKGROUND AND PURPOSE Genital infections due to Chlamydia trachomatis pose a considerable public health challenge worldwide and a vaccine is urgently needed to protect against these infections. We examined whether a vaccine composed of a combination of the major outer membrane protein (MOMP) and porin B protein (PorB) of C. trachomatis would have a protective advantage over a single subunit construct. METHODS Single and multisubunit vaccines expressing MOMP and PorB were constructed and evaluated in the mouse model of genital infection. Thus, groups of female C57BL/6 mice were immunized intramuscularly with recombinant Vibrio cholerae ghosts (VCG) expressing the vaccine antigens or VCG alone and humoral and cell-mediated immune responses were evaluated. RESULTS Significant levels of Chlamydia-specific secretory immunoglobulin A and immunoglobulin G2a were detected in vaginal washes and serum of immunized mice. The multisubunit construct induced a significantly higher level of T-helper Type 1 response than the single subunits as measured by the amount of interferon-gamma produced by immune T cells in response to re-stimulation with ultraviolet-irradiated elementary bodies in vitro. Three weeks after the last immunization, animals were challenged intravaginally with 10(7) inclusion-forming units of C. trachomatis serovar D. There was a significant difference in the intensity and duration of vaginal shedding between the vaccine-immunized mice and controls. All the animals immunized with the multisubunit vaccine had completely resolved the infection 2 weeks post-challenge. Higher numbers of embryos were observed in vaccinated animals than in controls, indicating protection against infertility. CONCLUSION These results underscore the potential, albeit moderate, vaccine advantage of the multisubunit formulation.
Serpin Induced Antiviral Activity of Prostaglandin Synthetase-2 against HIV-1 Replication

The serine protease inhibitors (serpins) are anti-inflammatory proteins that have various functions. By screening a diverse panel of viruses, we demonstrate that the serpin antithrombin III (ATIII) has a broad-spectrum anti-viral activity for HIV-1, HCV and HSV. To investigate the mechanism of action in more detail we investigated the HIV-1 inhibition. Using gene-expression arrays we found that multiple host cell signal transduction pathways were activated by ATIII in HIV-1 infected cells but not in uninfected controls. Moreover, the signal pathways initiated by ATIII treatment, were more than 200-fold increased by the use of heparin-activated ATIII. The most up-regulated transcript in HIV-1 infected cells was prostaglandin synthetase-2 (PTGS2). Furthermore, we found that over-expression of PTGS2 reduced levels of HIV-1 replication in human PBMC. These findings suggest a central role for serpins in the host innate anti-viral response. Host factors such as PTGS2 elicited by ATIII treatment could be exploited in the development of novel anti-viral interventions.
Slicing, I/O and the Implicit State

Program slicing consists of deleting statements from a program, creating a reduced program, a slice, that preserves the original program’s behaviour for a given set of variables at a chosen point in the program. However, some aspects of a program’s semantics are not captured by a set of variables, rendering slicing inapplicable to their analysis. These aspects of the program’s state shall, collectively, be termed the ‘implicit state’. For example, the input list supplied to a program is not denoted by a variable, rather it is part of the implicit state. It will be shown that this implicitness causes existing slicing algorithms to produce incorrect slices with respect to input. In order to solve the problem the program to be sliced will be transformed into an ‘explicit’ version (in which all aspects of its semantics are captured by variables). The approach is also applied to a wider class of problems in which slicing is inhibited by the lack of variables upon which to form a suitable slicing criterion. Because the approach can be expressed as a source–level transformation, it has the attractive property that the slicing algorithm need not be altered.
Right-permutative cellular automata on topological Markov chains

In this paper we consider cellular automata $(G,\Phi)$ with algebraic local rules and such that $G$ is a topological Markov chain which has a structure compatible to this local rule. We characterize such cellular automata and study the convergence of the Cesaro mean distribution of the iterates of any probability measure with complete connections and summable decay.
Smart glasses with a peripheral vision display

We present a demonstration of an initial peripheral vision glasses prototype. We can display patterns in the peripheral vision of the user. A simple use case is to show notifications. Up to 8 different notification types can be distinguished. We also suggest to use it to modify walking speed of users (depending on the animations people tend to speed up or slow down).
Effect of Phacoemulsification on Corneal Endothelium in Type 2 Effect of Phacoemulsification on Corneal Endothelium in Type 2 Diabetic Patients versus Normal Patients Phacoemulsification on Diabetic Patients versus Normal Patients Phacoemulsification on Corneal Endothelium Corneal Endothelium

Objective : This study aims to assess how phacoemulsi ﬁ cation affects individuals with type 2 diabetes and normal corneal endothelium. Patients and methods : This work involved 80 eyes of 80 individuals having surgery of cataract, classi ﬁ ed into two equal groups, each of 40 eyes; group (1) with (T2DM) and group (2) without DM. After a full ophthalmic examination, the specular microscopic examination was performed for the determination of endothelial cell density. Results : One month after surgery, a comparison between the two study groups revealed statistically insigni ﬁ cant differences in either group ' s central corneal thickness (CCT), coef ﬁ cient of variation (CV%), or corneal endothelial cell density (ECD). However, their hexagonality (Hex) showed a signi ﬁ cant difference ( P ¼ 0.021) in comparison between group (1 and 2). There is a signi ﬁ cant decrease in ECD in both groups after one month of phaco surgery with a highly signi ﬁ cant decrease in diabetic than non-diabetic groups ( P < 0.001). The same was observed in Hex and CV%. Also, CCT was increased in both groups, more in the diabetic group (1) with highly statistically signi ﬁ cance at ( P < 0.001). Conclusion : From this study, phacoemulsi ﬁ cation decreases the corneal endothelial cell count, and type 2 DM facilitate this process and leads to more decrease in their density. Especially in diabetic individuals, phacoemulsi ﬁ cation procedures might cause damage to corneal endothelial cells. Since diabetes individuals have impaired endothelial wound healing, maintaining endothelial cell health is crucial.
The Art of HIV Elimination: Past and Present Science.

INTRODUCTION Remarkable strides have been made in controlling the HIV epidemic, although not enough to achieve epidemic control. More recently, interest in biomedical HIV control approaches has increased, but substantial challenges with the HIV cascade of care hinder successful implementation. We summarise all available HIV prevention methods and make recommendations on how to address current challenges. DISCUSSION In the early days of the epidemic, behavioural approaches to control the HIV dominated, and the few available evidence-based interventions demonstrated to reduce HIV transmission were applied independently from one another. More recently, it has become clear that combination prevention strategies targeted to high transmission geographies and people at most risk of infections are required to achieve epidemic control. Biomedical strategies such as male medical circumcision and antiretroviral therapy for treatment in HIV-positive individuals and as pre-exposure prophylaxis in HIV-negative individuals provide immense promise for the future of HIV control. In resource-rich settings, the threat of HIV treatment optimism resulting in increased sexual risk taking has been observed and there are concerns that as ART roll-out matures in resource-poor settings and the benefits of ART become clearly visible, behavioural disinhibition may also become a challenge in those settings. Unfortunately, an efficacious vaccine, a strategy which could potentially halt the HIV epidemic, remains elusive. CONCLUSION Combination HIV prevention offers a logical approach to HIV control, although what and how the available options should be combined is contextual. Therefore, knowledge of the local or national drivers of HIV infection is paramount. Problems with the HIV care continuum remain of concern, hindering progress towards the UNAIDS target of 90-90-90 by 2020. Research is needed on combination interventions that address all the steps of the cascade as the steps are not independent of each other. Until these issues are addressed, HIV elimination may remain an unattainable goal.
The HIV-1 protease substitution K55R: a protease-inhibitor-associated substitution involved in restoring viral replication.

OBJECTIVES The identification and in vitro characterization of novel protease mutations strongly associated with known protease resistance mutations. METHODS The association between pairs of protease amino acid substitutions was identified using a database of protease sequences derived from protease inhibitor-experienced patients (n = 803). In vitro characterization included drug susceptibility and viral replication studies performed on recombinant viruses harbouring site-directed mutations. RESULTS The K55R mutation, which is not a natural polymorphism, was identified to be strongly associated with protease mutations M46I/L and to a lesser extent L24I, I54V and V82A/T/S/F. In vitro characterization of the K55R substitution indicated a primary role for this substitution in increasing replicative capacity in the presence of specific protease mutations. CONCLUSIONS The K55R mutation is a secondary drug resistance mutation that can improve viral replication capacity in the presence of other primary protease mutations.
Ibuprofen-Induced Hypokalemia and Distal Renal Tubular Acidosis: A Patient's Perceptions of Over-the-Counter Medications and Their Adverse Effects

We highlight a case of distal renal tubular acidosis secondary to ibuprofen and codeine use. Of particular interest in this case are the patient's perception of over-the-counter (OTC) medication use, her own OTC use prior to admission, and her knowledge of adverse reactions or side effects of these medications prior to taking them.