Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversification trajectories and evolutionary life-history traits in early sharks and batoids

Different interpretations on the timing of early diversification and radiation of modern sharks and batoids (Neoselachii) in the Earth's history exist and are related to discrepancies in taxonomic and phylogenetic interpretations favouring a Late Triassic or earliest Jurassic diversification and subsequent radiation event, respectively. Sampling standardization based on pooled taxonomic occurrences made it possible to overcome the problem of a much richer neoselachian record in the Late Jurassic than earlier on. The standardized pattern of genus richness is one of low and fairly constant diversity in the Late Triassic and earliest Jurassic with a steep rise in the Toarcian (ca 180 Myr ago), representing the maximum diversification rate in the Jurassic towards a Middle and Late Jurassic plateau. The major Toarcian diversification agrees with the conclusions based on phylogenetic analyses, but is in conflict with older interpretations based on raw data. Early Jurassic expansion of neoselachians was opportunistic in the aftermath of the end-Triassic mass extinction and the reasons for their rapid diversification and radiation probably include small body size, short lifespans and oviparity, enabling faster ecological reorganizations and innovations in body plans for adapting to changing environmental conditions.
Should living-unrelated renal transplant recipients receive antibody induction? Results of a clinical experience trial

Background. Living-donor kidney transplant recipients generally do not receive antibody induction. Induction avoidance may not be appropriate, particularly for living-unrelated renal transplant (LURT) recipients, in whom matching may not be optimal. We compared the incidence of acute rejection and graft outcome of LURT recipients who were administered no induction and cadaveric renal transplant (CRT) recipients who were administered anti-CD25 antibody. These groups both had immediate graft function and similar maintenance immunosuppression. Methods. This retrospective analysis included patients who received kidney transplants between 1999 and 2000. CRT recipients received basiliximab, corticosteroids, mycophenolate mofetil (MMF), and delayed tacrolimus (serum creatinine <3 mg/dL). LURT recipients received tacrolimus (initiated pretransplantation), MMF, and corticosteroids. Results. The analysis included 136 LURT recipients and 126 CRT recipients. CRT recipients included more African Americans (52.4% vs. 30.9%, P <0.01). LURT recipients included more patients with at least one human leukocyte antigen mismatch (97.8% vs. 85.7%, P <0.01). A higher acute rejection rate was observed in LURT recipients at both 6 months (LURT recipients 19.1% vs. CRT recipients 3.2%, P <0.01) and 1 year (21.3% vs. 4.0%, P <0.0004); a higher rate also was observed in African American LURT recipients compared with African American CRT recipients (35.7% vs. 4.5%, P <0.0015) at 1 year. LURT recipients demonstrated a threefold greater rejection risk than CRT recipients who were administered basiliximab (relative risk: 3.6, P <0.002). Graft survival was similar at 1 year. Conclusion. The higher rejection rates in LURT recipients (no induction) compared with CRT recipients (basiliximab induction), despite similar chronic immunosuppression (tacrolimus, MMF, and steroids) and immediate graft function, indicate the potential advantage of anti-CD25 induction in LURT protocols to reduce the risk of acute rejection.
A tight lower bound on the classical communication cost of entanglement dilution

Suppose two distant observers, Alice and Bob, share some form of entanglement - quantum correlations - in some bipartite pure quantum states. They may apply local operations and classical communication to convert one form of entanglement to another. Since entanglement is regarded as a resource in quantum information processing, it is an important question to ask how much classical communication, which is also a resource, is needed in the inter-conversion process of entanglement. In this paper, we address this important question in the many-copy case. The inter-conversion process of entanglement is usually divided into two types: concentrating the entanglement from many partially entangled states into a smaller number of maximally entangled states (i.e., singlets) and the reverse process of diluting singlets into partially entangled states. It is known that entanglement concentration requires no classical communication, but the best prior art result for diluting to N copies of a partially entangled state requires an amount of communication on the order of /spl radic/N. Our main result is to prove that this prior art result is optimal up to a constant factor; any procedure for approximately creating N partially entangled states from singlets requires /spl Omega/(/spl radic/N) bits of classical communication. Previously not even a constant bound was known for approximate entanglement transformations. We also prove a lower bound on the inefficiency of the process: to dilute singlets to N copies of a partially entangled state, the entropy of entanglement must decrease by /spl Omega/(/spl radic/N). Moreover, we introduce two new tools - /spl delta/-significant subspaces and the standard form protocol reduction in entanglement manipulations. We hope that these two new tools will be useful in other work in quantum information theory.
Operation context and context-based operational transformation

Operational Transformation (OT) is a technique for consistency maintenance and group undo, and is being applied to an increasing number of collaborative applications. The theoretical foundation for OT is crucial in determining its capability to solve existing and new problems, as well as the quality of those solutions. The theory of causality has been the foundation of all prior OT systems, but it is inadequate to capture essential correctness requirements. Past research had invented various patches to work around this problem, resulting in increasingly intricate and complicated OT algorithms. After having designed, implemented, and experimented with a series of OT algorithms, we reflected on what had been learned and set out to develop a new theoretical framework for better understanding and resolving OT problems, reducing its complexity, and supporting its continual evolution. In this paper, we report the main results of this effort: the theory of operation context and the COT (Context-based OT) algorithm. The COT algorithm is capable of supporting both do and undo of any operations at anytime, without requiring transformation functions to preserve Reversibility Property, Convergence Property 2, Inverse Properties 2 and 3. The COT algorithm is not only simpler and more efficient than prior OT control algorithms, but also simplifies the design of transformation functions. We have implemented the COT algorithm in a generic collaboration engine and used it for supporting a range of novel collaborative applications.
Cre‐expressing neurons in visual cortex of Ntsr1‐Cre GN220 mice are corticothalamic and are depolarized by acetylcholine

The Ntsr1‐Cre GN220 mouse expresses Cre‐recombinase in corticothalamic (CT) neurons in neocortical layer 6. It is not known if the other major types of pyramidal neurons in this layer also express this enzyme. By electrophysiological recordings in slices and histological analysis of the uptake of retrogradely transported beads we show that Cre‐positive neurons are CT and not corticocortical or corticoclaustral types. Furthermore, we show that Ntsr1‐Cre‐positive cells are immuno‐positive for the nuclear transcription factor Forkhead box protein P2 (FoxP2). We conclude that Cre‐expression is limited to a specific type of pyramidal neuron: CT. However, it appears as not all CT neurons are Cre‐expressing; there are indications that the penetrance of the gene is about 90%. We demonstrate the utility of assigning a specific identity to individual neurons by determining that the CT neurons are potently modulated by acetylcholine acting on both nicotinic and muscarinic acetylcholine receptors. These results corroborate the suggested function of these neurons in regulating the gain of thalamocortical transfer of sensory information depending on attentional demand and state of arousal.
Emergence cerebral oxygen desaturation without hemodynamic compromise in pediatric patients

Background The regional cerebral oxygen saturation (rSO2) decreases significantly during ordinary anesthetic recovery in pediatric patients anesthetized with sevoflurane or desflurane. The present study examined the relationship between rSO2 and the clinical parameters associated with the degree of anesthetic recovery. Methods Twelve pediatric patients with American Society of Anesthesiologists physical status 1 were assigned randomly to receive anesthesia with sevoflurane or desflurane. All children underwent general anesthesia for minor surgery. After surgery, the rSO2, the age-adjusted MAC fraction of anesthetic concentration (FE), and the bispectral index (BIS) were recorded over a 10-minute period. The correlations between rSO2 and candidate predictors, such as FE, BIS, anesthetic, and duration of anesthesia, were analyzed. Results All children recovered uneventfully. The lowest observed rSO2 reached 63% and the maximum decrease in rSO2 was 24%. The mean blood pressure and heart rate were maintained within clinical ranges. The decrease in rSO2 correlated positively with the FE (r = 0.25, P = 0.00) and the duration of anesthesia (r = 0.24, P = 0.01), and inversely with the use of sevoflurane (r = -0.30, P = 0.00). Conclusions Despite normal parameters, cerebral desaturation occurred during the emergence of ordinary general anesthesia even without hemodynamic compromise or arterial desaturation. Cerebral desaturation might be associated with the degree of anesthetic recovery and the use of sevoflurane.
Light Scattering Study of the Formation and Structure of Partially Hydrolyzed Poly(acrylamide)/Calcium(II) Complexes

The Ca2+ concentration and hydrolysis degree [−COO-] dependence of the self-complexation of partially hydrolyzed poly(acrylamide) (HPAM) chains in CaCl2 aqueous solution was systematically investigated by a combination of static and dynamic laser light scattering. We have, for the first time, revealed a transition between the intrachain and interchain complexations. For each given HPAM sample, there exists a critical Ca2+ concentration ([Ca2+]agg) at which the interchain HPAM complexation becomes dominant. [Ca2+]agg is related to [−COO-] by [Ca2+]agg = 7.46 × 10-9 [−COO-]-1.4, indicating that the complexation is not stoichiomeric and many Ca2+ ions are free in water. We also found that even at [Ca2+] > [Ca2+]agg, the complexation at the initial stage was mainly an intrachain process, but gradually evolved into an interchain aggregation. The length of the initial stage increases as [−COO-] and [Ca2+] decrease. Our results showed that in the complexation process, the weight average molecular weight (Mw) of .
Identification and Analysis of the Acyl Carrier Protein (ACP) Docking Site on β-Ketoacyl-ACP Synthase III*

The molecular details that govern the specific interactions between acyl carrier protein (ACP) and the enzymes of fatty acid biosynthesis are unknown. We investigated the mechanism of ACP·protein interactions using a computational analysis to dock the NMR structure of ACP with the crystal structure of β-ketoacyl-ACP synthase III (FabH) and experimentally tested the model by the biochemical analysis of FabH mutants. The activities of the mutants were assessed using both an ACP-dependent and an ACP-independent assay. The ACP interaction surface was defined by mutations that compromised FabH activity in the ACP-dependent assay but had no effect in the ACP-independent assay. ACP docked to a positively charged/hydrophobic patch adjacent to the active site tunnel on FabH, which included a conserved arginine (Arg-249) that was required for ACP docking. Kinetic analysis and direct binding studies between FabH and ACP confirmed the identification of Arg-249 as critical for FabH·ACP interaction. Our experiments reveal the significance of the positively charged/hydrophobic patch located adjacent to the active site cavities of the fatty acid biosynthesis enzymes and the high degree of sequence conservation in helix II of ACP across species.
Microbial Community Diversity Associated with Carbon and Nitrogen Cycling in Permeable Shelf Sediments

ABSTRACT Though a large fraction of primary production and organic matter cycling in the oceans occurs on continental shelves dominated by sandy deposits, the microbial communities associated with permeable shelf sediments remain poorly characterized. Therefore, in this study, we provide the first detailed characterization of microbial diversity in marine sands of the South Atlantic Bight through parallel analyses of small-subunit (SSU) rRNA gene (Bacteria), nosZ (denitrifying bacteria), and amoA (ammonia-oxidizing bacteria) sequences. Communities were analyzed by parallel DNA extractions and clone library construction from both sediment core material and manipulated sediment within column experiments designed for geochemical rate determinations. Rapid organic-matter degradation and coupled nitrification-denitrification were observed in column experiments at flow rates resembling in situ conditions over a range of oxygen concentrations. Numerous SSU rRNA phylotypes were affiliated with the phyla Proteobacteria (classes Alpha-, Delta-, and Gammaproteobacteria), Planctomycetes, Cyanobacteria, Chloroflexi, and Bacteroidetes. Detectable sequence diversity of nosZ and SSU rRNA genes increased in stratified redox-stabilized columns compared to in situ sediments, with the Alphaproteobacteria comprising the most frequently detected group. Alternatively, nitrifier communities showed a relatively low and stable diversity that did not covary with the other gene targets. Our results elucidate predominant phylotypes that are likely to catalyze carbon and nitrogen cycling in marine sands. Although overall diversity increased in response to redox stabilization and stratification in column experiments, the major phylotypes remained the same in all of our libraries, indicating that the columns sufficiently mimic in situ conditions.
A Formal Study of Collaborative Access Control in Distributed Datalog

We formalize and study a declaratively specified collaborative access control mechanism for data dissemination in a distributed environment. Data dissemination is specified using distributed datalog. Access control is also defined by datalog-style rules, at the relation level for extensional relations, and at the tuple level for intensional ones, based on the derivation of tuples. The model also includes a mechanism for " declassifying " data, that allows circumventing overly restrictive access control. We consider the complexity of determining whether a peer is allowed to access a given fact, and address the problem of achieving the goal of disseminating certain information under some access control policy. We also investigate the problem of information leakage, which occurs when a peer is able to infer facts to which the peer is not allowed access by the policy. Finally, we consider access control extended to facts equipped with provenance information, motivated by the many applications where such information is required. We provide semantics for access control with provenance, and establish the complexity of determining whether a peer may access a given fact together with its provenance. This work is motivated by the access control of the Webdamlog system, whose core features it formalizes.
Recurrent herpes zoster myelitis treated with human interferon alpha: a case report

Recurrent herpes zoster myelitis is very rare. However, a case was recently observed in our hospital. A 43‐year‐old woman developed myelitis 2 weeks after development of shingles. Her condition was improved by methylprednisolone. Seven months later, she developed myelitis after development of shingles again. Antibody against varicella‐zoster (VZV), increased in the serum, but was negative in the cerebrospinal fluid. Methylprednisolone was not sufficiently effective against this attack. The refractory sensory disturbance was improved by human interferon alpha (IFN‐α). Natural killer cell activity, the helper T‐cell/suppressor T‐cell ratio and the K/Λ ratio of B‐cells increased with clinical improvement. In this case, delayed‐type hypersensitivity after VZV infection played a role in the occurrence of myelopathy and clinical improvement resulted from the immunosuppressive effects of IFN‐α.
Strand specificity of mutagenic bypass replication of DNA containing psoralen monoadducts in a human cell extract

Psoralens are mutagenic compounds of vegetable origin that are used as photosensitizing agents in the treatment of various skin diseases, blood cell cancer, and autoimmune disorders. To study the mechanism of mutagenicity of psoralens in humans, we examined the efficiency and fidelity of simian virus 40 origin-dependent replication in a human cell extract of M13mp2 DNA randomly treated with the psoralen derivative 4'-hydroxymethyl-4,5',8-trimethyl psoralen plus UVA irradiation. Replication of DNA treated with variable amounts of 4'-hydroxymethyl-4,5',8-trimethyl psoralen and a fixed UVA fluence was inhibited in a concentration-dependent manner. However, covalently closed monomer-length circular replication products were observed. Product analysis by renaturing agarose gel electrophoresis after cross-linking with 250- to 280-nm UV light indicated that approximately 1 of 9 psoralen monoadducts was bypassed during in vitro replication. Introduction of product DNA into Escherichia coli to score replication errors in the lacZalpha reporter gene demonstrated that replication of the damaged DNA was more mutagenic than was replication of undamaged DNA. Sequence analysis of lacZ mutants revealed that damage-dependent replication errors were predominantly T.A-->C.G transitions, transversions at C.G base pairs, and deletions of single A.T base pairs, the last occurring most frequently in homopolymeric runs. A comparison of error specificities with two substrates having the replication origin asymmetrically placed on opposite sides of the mutational target suggests that the lagging-strand replication apparatus is less accurate than the leading-strand replication apparatus for psoralen monoadduct-dependent deletion errors. A model is proposed based on the preferential loopout of the monoadducted base from the strand that templates retrograde discontinuous synthesis.
Formation rules of single phase solid solution in high entropy alloys

A new empirical rule to form single phase solid solution structured high entropy alloys was proposed by integrating three dependent parameters, i.e. atomic size difference δ, mixing enthalpy ΔHmix and valence electron concentration VEC. It was found that the single phase face centred cubic solid solution will form if δ < 4.27%, − 7.27 kJ mol− 1 < ΔHmix < 4 kJ mol− 1 and VEC>8, while the single phase body centred cubic solid solution will form in the case of δ < 4.27%, − 7.27 kJ mol− 1 < ΔHmix < 4 kJ mol− 1 and VEC < 6.87. This empirical rule was verified by typical high entropy alloys that have been reported.
Early Administration of Carvedilol Protected against Doxorubicin-Induced Cardiomyopathy

This study tested for the benefits of early administration of carvedilol as protection against doxorubicin (DOX)-induced cardiomyopathy. Thirty male, adult B6 mice were categorized into group 1 (untreated control), group 2 [DOX treatment (15 mg/every other day for 2 weeks, i.p.], and group 3 [carvedilol (15 mg/kg/d, from day 7 after DOX treatment for 28 days)], and euthanized by day 35 after DOX treatment. By day 35, the left ventricular ejection fraction (LVEF) was significantly lower in group 2 than in groups 1 and 3, and significantly lower in group 3 than in group 1, whereas the left ventricular (LV) end-diastolic and LV end-systolic dimensions showed an opposite pattern to the LVEF among the three groups. The protein expressions of fibrotic (Smad3, TGF-β), apoptotic (BAX, cleaved caspase 3, PARP), DNA damage (γ-H2AX), oxidative stress (oxidized protein), mitochondrial damage (cytosolic cytochrome-C), heart failure (brain natriuretic peptide), and hypertrophic (β-MHC) biomarkers of the LV myocardium showed an opposite pattern to the LVEF among the three groups. The protein expressions of antifibrotic (BMP-2, Smad1/5), α-MHC, and phosphorylated-Akt showed an identical pattern to the LVEF among the three groups. The microscopic findings of fibrotic and collagen-deposition areas and the numbers of γ-H2AX+ and 53BP1+ cells in the LV myocardium exhibited an opposite pattern, whereas the numbers of endothelial cell (CD31+, vWF+) markers showed an identical pattern to the LVEF among the three groups. Cardiac stem cell markers (C-kit+ and Sca-1+ cells) were significantly and progressively increased from group 1 to group 3. Additionally, the in vitro study showed carvedilol treatment significantly inhibited DOX-induced cardiomyoblast DNA (CD90/XRCC1+, CD90/53BP1+, and r-H2AX+ cells) damage. Early carvedilol therapy protected against DOX-induced DNA damage and cardiomyopathy.
The world‐wide ‘fast–slow’ plant economics spectrum: a traits manifesto

The leaf economics spectrum (LES) provides a useful framework for examining species strategies as shaped by their evolutionary history. However, that spectrum, as originally described, involved only two key resources (carbon and nutrients) and one of three economically important plant organs. Herein, I evaluate whether the economics spectrum idea can be broadly extended to water – the third key resource –stems, roots and entire plants and to individual, community and ecosystem scales. My overarching hypothesis is that strong selection along trait trade‐off axes, in tandem with biophysical constraints, results in convergence for any taxon on a uniformly fast, medium or slow strategy (i.e. rates of resource acquisition and processing) for all organs and all resources. Evidence for economic trait spectra exists for stems and roots as well as leaves, and for traits related to water as well as carbon and nutrients. These apply generally within and across scales (within and across communities, climate zones, biomes and lineages). There are linkages across organs and coupling among resources, resulting in an integrated whole‐plant economics spectrum. Species capable of moving water rapidly have low tissue density, short tissue life span and high rates of resource acquisition and flux at organ and individual scales. The reverse is true for species with the slow strategy. Different traits may be important in different conditions, but as being fast in one respect generally requires being fast in others, being fast or slow is a general feature of species. Economic traits influence performance and fitness consistent with trait‐based theory about underlying adaptive mechanisms. Traits help explain differences in growth and survival across resource gradients and thus help explain the distribution of species and the assembly of communities across light, water and nutrient gradients. Traits scale up – fast traits are associated with faster rates of ecosystem processes such as decomposition or primary productivity, and slow traits with slow process rates. Synthesis. Traits matter. A single ‘fast–slow’ plant economics spectrum that integrates across leaves, stems and roots is a key feature of the plant universe and helps to explain individual ecological strategies, community assembly processes and the functioning of ecosystems.