Miracle-dz/UniFAR-FTUs huggingface dataset:
PP32 and SET/TAF-Iβ proteins regulate the acetylation of newly synthesized histone H4

Abstract Newly synthesized histones H3 and H4 undergo a cascade of maturation steps to achieve proper folding and to establish post-translational modifications prior to chromatin deposition. Acetylation of H4 on lysines 5 and 12 by the HAT1 acetyltransferase is observed late in the histone maturation cascade. A key question is to understand how to establish and regulate the distinct timing of sequential modifications and their biological significance. Here, we perform proteomic analysis of the newly synthesized histone H4 complex at the earliest time point in the cascade. In addition to known binding partners Hsp90 and Hsp70, we also identify for the first time two subunits of the histone acetyltransferase inhibitor complex (INHAT): PP32 and SET/TAF-Iβ. We show that both proteins function to prevent HAT1-mediated H4 acetylation in vitro. When PP32 and SET/TAF-Iβ protein levels are down-regulated in vivo, we detect hyperacetylation on lysines 5 and 12 and other H4 lysine residues. Notably, aberrantly acetylated H4 is less stable and this reduces the interaction with Hsp90. As a consequence, PP32 and SET/TAF-Iβ depleted cells show an S-phase arrest. Our data demonstrate a novel function of PP32 and SET/TAF-Iβ and provide new insight into the mechanisms regulating acetylation of newly synthesized histone H4.
HSOA Journal of Emergency Medicine, Trauma and Surgical Care

Monoclonal anti-CD47 therapy is a new form of immunotherapy, which has been used in a clinical setting in recent years for the treat-ment of haematological and solid malignancies. Anti-CD47 functions by blocking the CD47-SIRPα interaction and promotes the phago - cytosis of cancer cells, which attempt to invade the immune systems mechanisms via this interface. This review aims to highlight the significance of anaemia and thrombocytopenia associated with an - ti-CD47 therapy, as the expression of CD47 on healthy cells can lead to premature removal by phagocytes. Using the Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines, eligible studies formed the basis of this systematic review. The screening process of the literature was conducted in multiple phases and studies were considered relevant if the data fit the specified eligibility criteria. Of the original 395 reports obtained, 7 eligible clinical trials were used as they contained relevant statistical data for comparison. Using a proportional, binary random-effects meta-analysis, the incidence of both anaemia and thrombocytopenia was considered significant with a p value < 0.001. Both plots were generated with a confidence interval of 95% [CI 0.207-0.445 anaemia; CI 0.075-0.259 thrombocytopenia]. Using the findings of this review, the occurrence of both anaemia and thrombocytopenia is significant in participants undergoing treatment with various forms of anti-CD47 therapies. However, large-scale studies should be considered in future to determine which specific anti-CD47 therapy can effectively promote the removal of cancer cells with limited adverse effects.
A model for matching and integrating heterogeneous relational biomedical databases schemas

Database integration aims at providing a uniform and consistent view called global schema, over a set of autonomous and heterogeneous data sources, so that data residing in different sources can be accessed as if it was in a single schema. The integration of data sources can be performed in two steps, a matching and a data transformation step. Schema matching, the focus of this paper, is a fundamental operation in the manipulation of schema in formatting match, which takes two schemas that correspond semantically to each other. Manually specifying schema matches is a tedious, time consuming, error-prone, and therefore expensive process, which is a growing problem given the rapidly increasing number of data sources to integrate. As systems become able to handle more complex databases and applications such as biomedical databases schemas, their schemas become large, further increasing the number of matches to be performed. Several solutions in solving the issues of schema matching have been proposed. However, these solutions are still limited as (i) they do not explore most of the available information related to schemas, (ii) the approaches rely strictly on the assumption that the schemas to be matched are from the same application domain, and (iii) the approaches either match schemas by comparing the strings of the elements' names or by checking if those names are synonyms. This paper addresses the above limitations by proposing a model for matching heterogeneous relational biomedical databases' schemas that further improves the results of the integration.
Hamiltonian analysis of non-chiral Plebanski theory and its generalizations

We consider the non-chiral, full Lorentz group-based Plebanski formulation of general relativity in its version that utilizes the Lagrange multiplier field Φ with ‘internal’ indices. The Hamiltonian analysis of this version of the theory turns out to be simpler than in the previously considered in the literature version with Φ carrying spacetime indices. We then extend the Hamiltonian analysis to a more general class of theories whose action contains scalar invariants constructed from Φ. Such theories have recently been considered in the context of unification of gravity with other forces. We show that these more general theories have six additional propagating degrees of freedom as compared to general relativity. This has not been appreciated in the literature treating them as being not much different from GR.
Craniofacial morphology of Chinese patients with bilateral temporomandibular joint osteoarthrosis.

OBJECTIVE To evaluate the morphological features of craniofacial structures in young patients affected by bilateral temporomandibular joint osteoarthrosis (TMJOA). METHODS Forty-three males and 189 females aged 15 to 25 years who had lateral cephalograms and temporomandibular joint (TMJ) radiological examinations were included. They were classified into a TMJOA group and a control group, according to TMJ bony status. Thirty-two variables from lateral cephalogram were analysed by t test to evaluate the cranial and dentofacial differences between the two groups. RESULTS TMJOA group showed a shorter posterior ramus height and shorter condyles, smaller SNB angle and larger ANB angle, smaller facial plane angle and larger angle of convexity, steeper mandibular plane angle and more vertical y-axis. CONCLUSION Bilateral TMJOA is associated with dentofacial alterations characterised by a tendency toward retrognathism and shorter mandibles. However, the cause-and-effect relationship is yet to be clarified.
Metal uptake in a peri-urban Lactuca sativa cultivated area

In this study, two Lactuca sativa crops grown in a net-protected site and an unprotected site were compared. The results showed metals were accumulated by Lactuca sativa. Higher metal accumulation in lettuce grown in the unprotected parcel was established, and the only significant differences in their physicochemical properties were cation exchange capacity and exposure to sunlight. Exposure to the sun may translate into higher soil–plant flux of water and/or higher decomposition rate of organic matter, which may augment the mobilization of metals into the plant, and therefore lead to higher noxious metal accumulation on the crops. Also, EDTA was explored as a possible extractant that could predict the bioavailablity of metals to the lettuce. Our results did not show a good agreement between the metal transferred from soil to leaves and the EDTA extracted metals, although some tendencies were found for the metal transfer from soil to roots. It is predicted that many developing countries will continue and/or increase the use of waste water for the irrigation of crops despite the health risks. Different solutions have been explored to diminish the availability of the metals in the soils. Our study shows that an action as simple as placing a net over the parcel could help diminish the accumulation of metals into the crops of a rapidly expanding peri-urban agricultural system.
5,6-Epoxyeicosatrienoic Acid Mediates the Enhanced Renal Vasodilation to Arachidonic Acid in the SHR

Abstract—We have shown a cytochrome P450–dependent renal vasodilator effect of arachidonic acid in response to inhibition of cyclooxygenase and elevation of perfusion pressure, which was enhanced in the spontaneously hypertensive rat (SHR) and linked to increased production of and/or responsiveness to epoxyeicosatrienoic acids (EETs). In the SHR, vasodilation elicited by low doses of arachidonic acid was attenuated by the nitric oxide synthase inhibitor Nw-nitro-l-arginine (50 &mgr;mol/L), whereas the responses to high doses were unaffected. Inhibition of epoxygenases with miconazole (0.3 &mgr;mol/L) in the presence of Nw-nitro-l-arginine greatly reduced the renal vasodilator response to all doses of arachidonic acid. Tetraethylammonium (10 mmol/L), a nonselective K+ channel blocker, abolished the nitric oxide–independent renal vasodilator effect of arachidonic acid as well as the vasodilator effect of 5,6-EET, confirming that EET-dependent vasodilation involves activation of K+ channels. Under conditions of elevated perfusion pressure (200 mm Hg) and cyclooxygenase inhibition, 5,6-EET, 8, 9-EET, and 11,12-EET caused renal vasodilatation in both SHR and Wistar-Kyoto rats (WKY), whereas 14,15-EET produced vasoconstriction. 5,6-EET was the most potent renal vasodilator of the EET regioisomers in the SHR by a factor of 4 or more. In the SHR, 5,6-EET- and 11,12-EET–induced renal vasodilatation was >2-fold greater than that registered in WKY. Thus, the augmented vasodilator responses to arachidonic acid in the SHR is through activation of K+ channels, and 5,6-EET is the most likely mediator.
Managing Urinary Continence Following Stroke: Can We Do Better?

Rationale : Urinary incontinence (UI) is a common consequence of stroke and the most significant indicator of poor outcome, yet continence management in many acute settings remains suboptimal. Objective : To examine local post stroke continence management practice within the context of the National Stroke Foundation guideline recommendations and to develop a solution that will improve post stroke continence care. Context : Three stroke rehabilitation units within Hunter New England Local Health District in regional NSW, Australia. Participants : Nursing staff working with stroke patients. Interventions : We carried out an audit to characterise current continence management practice, then developed a urinary continence assessment and management tool and an online modular continence learning package to support staff in their care of stroke patients with continence difficulties. Findings : Audit results showed a substantial evidence/practice gap across the three rehabilitation sites, including: a lack of continence assessments and individual management plans; a failure to recognise and document the specific urinary incontinence type; a tendency to adopt compensatory strategies rather than treat the underlying problem; and, a lack of multidisciplinary involvement in continence care. Conclusion : Our findings confirm the need for better post stroke continence management within this cohort and justify the need for a change in practice. It is envisaged that our standardised continence management protocol and web-based education program will support this practice change and improve continence levels and quality of life for patients experiencing urinary incontinence following stroke. Key Words : Audit, Australia, Continence, Evidence-based, Rehabilitation, Stroke, Urinary incontinence.
Non-Exercise Activity Thermogenesis: The Crouching Tiger Hidden Dragon of Societal Weight Gain

Non-exercise activity thermogenesis (NEAT) is the energy expenditure of all physical activities other than volitional sporting-like exercise. NEAT includes all the activities that render us vibrant, unique, and independent beings such as working, playing, and dancing. Because people of the same weight have markedly variable activity levels, it is not surprising that NEAT varies substantially between people by up to 2000 kcal per day. Evidence suggests that low NEAT may occur in obesity but in a very specific fashion. Obese individuals appear to exhibit an innate tendency to be seated for 2.5 hours per day more than sedentary lean counterparts. If obese individuals were to adopt the lean “NEAT-o-type,” they could potentially expend an additional 350 kcal per day. Obesity was rare a century ago and the human genotype has not changed over that time. Thus, the obesity epidemic may reflect the emergence of a chair-enticing environment to which those with an innate tendency to sit, did so, and became obese. To reverse obesity, we need to develop individual strategies to promote standing and ambulating time by 2.5 hours per day and also re-engineer our work, school, and home environments to render active living the option of choice.
PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.

As the number of protein folds is quite limited, a mode of analysis that will be increasingly common in the future, especially with the advent of structural genomics, is to survey and re-survey the finite parts list of folds from an expanding number of perspectives. We have developed a new resource, called PartsList, that lets one dynamically perform these comparative fold surveys. It is available on the web at http://bioinfo.mbb. yale.edu/partslist and http://www.partslist. org. The system is based on the existing fold classifications and functions as a form of companion annotation for them, providing 'global views' of many already completed fold surveys. The central idea in the system is that of comparison through ranking; PartsList will rank the approximately 420 folds based on more than 180 attributes. These include: (i) occurrence in a number of completely sequenced genomes (e.g. it will show the most common folds in the worm versus yeast); (ii) occurrence in the structure databank (e.g. most common folds in the PDB); (iii) both absolute and relative gene expression information (e.g. most changing folds in expression over the cell cycle); (iv) protein-protein interactions, based on experimental data in yeast and comprehensive PDB surveys (e.g. most interacting fold); (v) sensitivity to inserted transposons; (vi) the number of functions associated with the fold (e.g. most multi-functional folds); (vii) amino acid composition (e.g. most Cys-rich folds); (viii) protein motions (e.g. most mobile folds); and (ix) the level of similarity based on a comprehensive set of structural alignments (e.g. most structurally variable folds). The integration of whole-genome expression and protein-protein interaction data with structural information is a particularly novel feature of our system. We provide three ways of visualizing the rankings: a profiler emphasizing the progression of high and low ranks across many pre-selected attributes, a dynamic comparer for custom comparisons and a numerical rankings correlator. These allow one to directly compare very different attributes of a fold (e.g. expression level, genome occurrence and maximum motion) in the uniform numerical format of ranks. This uniform framework, in turn, highlights the way that the frequency of many of the attributes falls off with approximate power-law behavior (i.e. according to V(-b), for attribute value V and constant exponent b), with a few folds having large values and most having small values.
Physical, Chemical and Microbial Changes during the Composting of Conocarpus erectus Residues

Changes in physical, chemical and microbial parameters were monitored during the composting of Conocarpus erectus residues using a bioreactor. The residues (leaves and small stems) were collected, cut into small pieces and mixed. The C/N ratio of the mixture was 25.22. The moisture content was adjusted to 65% at the start of the experiment.The total volume of the bioreactor was 0.03 m 3 . Airflow was supplied at a rate of 10 L/min. The results showed that the temperature increased and reached its maximum (54 o C) after 36 hrs and then decreased to 26 o C. The final compost was odourless and black. The pH decreased from 6.50 to 6.35 after 3 days and then increased to 6.83. The electrical conductivity increased with time from 1.77 to 2.09 mS/cm. The organic matter decreased from 83.93 to 75.85% and the loss reached to 39.86% and followed the first-order kinetic equation. The C/N ratio decreased from 25.22 to 18.48. The mesophilic bacteria and fungi decreased after 3 days and then increased, whereas the thermophilic ones increased after 3 days and then decreased. It can be concluded that composting can be a suitable method for converting Conocarpus erectus residues into compost if the optimum conditions are performed.
Foundations of the C++ concurrency memory model

Currently multi-threaded C or C++ programs combine a single-threaded programming language with a separate threads library. This is not entirely sound [7]. We describe an effort, currently nearing completion, to address these issues by explicitly providing semantics for threads in the next revision of the C++ standard. Our approach is similar to that recently followed by Java [25], in that, at least for a well-defined and interesting subset of the language, we give sequentially consistent semantics to programs that do not contain data races. Nonetheless, a number of our decisions are often surprising even to those familiar with the Java effort:We (mostly) insist on sequential consistency for race-free programs, in spite of implementation issues that came to light after the Java work. We give no semantics to programs with data races. There are no benign C++ data races. We use weaker semantics for trylock than existing languages or libraries, allowing us to promise sequential consistency with an intuitive race definition, even for programs with trylock. This paper describes the simple model we would like to be able to provide for C++ threads programmers, and explain how this, together with some practical, but often under-appreciated implementation constraints, drives us towards the above decisions.
Targeting Neutrophils to Prevent Malaria-Associated Acute Lung Injury/Acute Respiratory Distress Syndrome in Mice

Malaria remains one of the greatest burdens to global health, causing nearly 500,000 deaths in 2014. When manifesting in the lungs, severe malaria causes acute lung injury/acute respiratory distress syndrome (ALI/ARDS). We have previously shown that a proportion of DBA/2 mice infected with Plasmodium berghei ANKA (PbA) develop ALI/ARDS and that these mice recapitulate various aspects of the human syndrome, such as pulmonary edema, hemorrhaging, pleural effusion and hypoxemia. Herein, we investigated the role of neutrophils in the pathogenesis of malaria-associated ALI/ARDS. Mice developing ALI/ARDS showed greater neutrophil accumulation in the lungs compared with mice that did not develop pulmonary complications. In addition, mice with ALI/ARDS produced more neutrophil-attracting chemokines, myeloperoxidase and reactive oxygen species. We also observed that the parasites Plasmodium falciparum and PbA induced the formation of neutrophil extracellular traps (NETs) ex vivo, which were associated with inflammation and tissue injury. The depletion of neutrophils, treatment with AMD3100 (a CXCR4 antagonist), Pulmozyme (human recombinant DNase) or Sivelestat (inhibitor of neutrophil elastase) decreased the development of malaria-associated ALI/ARDS and significantly increased mouse survival. This study implicates neutrophils and NETs in the genesis of experimentally induced malaria-associated ALI/ARDS and proposes a new therapeutic approach to improve the prognosis of severe malaria.
Fetal Human Cytomegalovirus Transmission Correlates with Delayed Maternal Antibodies to gH/gL/pUL128-130-131 Complex during Primary Infection

Primary human cytomegalovirus (HCMV) infections during pregnancy are associated with a high risk of virus transmission to the fetus. To identify correlates of intrauterine HCMV transmission, serial serum samples from HCMV transmitter and non-transmitter pregnant women with primary HCMV infection were analyzed for the presence of neutralizing antibodies against different glycoproteins and glycoprotein complexes, which are known to mediate entry into distinct types of host cells. Neutralizing activity was detected in the sera early after primary infection; absorption with a soluble pentameric complex formed by gH/gL/pUL128-131, but not with gH/gL dimer or with gB, abolished the capacity of sera to neutralize infection of epithelial cells. Importantly, an early, high antibody response to pentamer antigenic sites was associated with a significantly reduced risk of HCMV transmission to the fetus. This association is consistent with the high in vitro inhibition of HCMV infection of epithelial/endothelial cells as well as cell-to-cell spreading and virus transfer to leukocytes by anti-pentamer antibodies. Taken together, these findings indicate that the HCMV pentamer complex is a major target of the antibody-mediated maternal immunity.
Non-tidal ocean loading signals of the North and Baltic Sea from terrestrial gravimetry, GNSS, and high-resolution modeling

Non-tidal ocean loading signals are known to be a signiﬁcant source of geophysically induced noise in gravimetric and geodetic observations also far-away from the coast and especially during extreme events such as storm surges. Operational products suﬀer from a low temporal and spatial resolution and reveal only small amplitudes on continental stations. Dedicated high-resolution sea-level modelling of the North and Baltic Sea provides a largely improved prediction of non-tidal ocean loading signals. Superconducting gravimeter and GNSS observations on the small oﬀshore island of Heligoland in the North Sea are used for a thorough evaluation of the model values revealing correlations of up to 0.9 and signal reductions of up to 50 % during a storm surge period of one month in Jan-Feb 2022. Additional continental superconducting gravimeter stations are used to assess the beneﬁts from high-resolution modelling for an improved signal separation further away from the coast.
A Simple Way to Initialize Recurrent Networks of Rectified Linear Units

Learning long term dependencies in recurrent networks is difficult due to vanishing and exploding gradients. To overcome this difficulty, researchers have developed sophisticated optimization techniques and network architectures. In this paper, we propose a simpler solution that use recurrent neural networks composed of rectified linear units. Key to our solution is the use of the identity matrix or its scaled version to initialize the recurrent weight matrix. We find that our solution is comparable to LSTM on our four benchmarks: two toy problems involving long-range temporal structures, a large language modeling problem and a benchmark speech recognition problem.
Measuring Beliefs in an Experimental Lost Wallet Game

Abstract We measure beliefs in an experimental game. Player 1 may take x x (our treatment variable), the more likely is player 1 to take the x . Out of those who leave the x , many expect to get back less than x . There is no positive correlation between x and the amount y that 2 allocates to 1. However, there is positive correlation between y and 2's expectation of 1's expectation of y . Journal of Economic Literature Classification Numbers: C72, C92.