gebhart/patrepeval huggingface dataset:
Parameter estimation problems with singular information matrices (2001)

The case of a singular Fisher information matrix (FIM) represents a significant complication for the theory of the Cramer-Rao lower bound (CRB) that is usually handled by resorting to the pseudoinverse of the Fisher matrix. We take a different approach in which the CRB is derived as the solution to an unconstrained quadratic maximization problem, which enables us to handle the singular case in a simple yet rigorous manner. When the Fisher matrix is singular, except under unusual circumstances, any estimator having the specified bias derivatives that figure in the CRB must have infinite variance.
Alkali-Alumina Sorbents for Regenerable SO_2 Removal in Fluidized-Coal Combustion (1985)

Sodium and sodium-lithium oxides supported on porous alumina have been investigated as regenerable SO_2 sorbents for fluidized coal combustion. In adsorption the oxides are converted to sulfates. In regeneration, carried out by reduction with CO, the sulfates are converted back to oxides while sulfur is removed in elemental form (S_2), SO_2 and COS. The transient composition of sorbent and gaseous products was measured in a thermogravimetric analyzer and a packed-bed microreactor in order to delineate the basic chemistry of regeneration and determine conditions that maximize the yield of elemental sulfur.
Relationship between anterior capsule contraction and posterior capsule opacification after cataract surgery in patients with diabetes mellitus (2005)

Hayashi et al.1 have demonstrated the absence of a correlation between contraction of the anterior capsule opening and the density of posterior capsule opacification (PCO) 1 year after uneventful phacoemulsification and acrylic foldable intraocular lens implantation in patients with diabetes mellitus. In any study of PCO, the fundamental issue is the objective documentation of opacification.2 In the study by Hayashi et al., Scheimpflug videography measuring slit images over only small areas of the posterior capsule was used. Scheimpflug videography is good for indicating PCO severity and has good correlation with patients' visual acuity. It, however, has the drawback that any areas of involvement beyond the meridians of analysis may be missed and a significant portion of off-meridian PCO is overlooked thereafter. The overexpression or underexpression of the results may affect our understanding of the etiology or pathogenesis of PCO.2 Another downside of this study is the failure to address the natural progression of PCO and the exact timeframe of measurement. Posterior capsule opacification usually begins with capsule fibrosis, gradually evolving into Elschnig pearls.3,4 According to Hayashi et al., only capsule fibrosis is the common pathogenesis underpinning both anterior capsule opening contraction and PCO formation.1 However, the 1-year Scheimpflug videography findings revealed pearl-type PCO rather than capsule fibrosis.1 This observation was believed to be the major cause of the lack of a correlation over time.1 It is important to note that the PCO imaging system adopted, Scheimpflug videography, might not be able to detect progression, as pointed out by Aslam et al.5 and Friedman et al.6 More sensitive and specific methods of capturing PCO, including Tetz's computerized analysis of density boundaries and the density map system of Friedman et al. should be considered as viable alternates. Finally, Hayashi et al. conclude that contraction of the anterior capsule opening and PCO after cataract surgery cannot be explained by a common mechanism. We do not concur with the authors' interpretation of correlation coefficient. The absence of a positive or negative correlation between 2 variables cannot extirpate the possibility that both are under the direct influence of a common mechanism, pathogenesis, or unobserved factor. There could have been many confounding factors influencing the variables to different extents and magnitudes. One of them was the protective effect of an acrylic foldable IOL, which has been shown to lower the PCO rate significantly. We do not think the authors' conclusion cannot be drawn or implied objectively and logically from the observed results. David T.L. Liu MRCS Vesta C.K. Chan MB ChB Wai-Man Chan FRCP, FRCS Dennis S.C. Lam MD, FRCOphth Hong Kong, China
Construction of Panel Data Through Record Linkage: Application to Hungarian Budget Surveys: 1987, 89, 91 (1996)

This note describes the matching procedure used to construct panel data sets from the 1987, 1989 and 1991 Hungarian Household Budget servey samples.
Determining the clinical importance of treatment benefits for interventions for painful orthopedic conditions (2015)

The overarching goals of treatments for orthopedic conditions are generally to improve or restore function and alleviate pain. Results of clinical trials are generally used to determine whether a treatment is efficacious; however, a statistically significant improvement may not actually be clinically important, i.e., meaningful to the patient. To determine whether an intervention has produced clinically important benefits requires a two-step process: first, determining the magnitude of change considered clinically important for a particular measure in the relevant population and, second, applying this yardstick to a patient's data to determine whether s/he has benefited from treatment. Several metrics have been devised to quantify clinically important differences, including the minimum clinically important difference (MCID) and clinically important difference (CID). Herein, we review the methods to generate the MCID and other metrics and their use and interpretation in clinical trials and practice. We particularly highlight the many pitfalls associated with the generation and utilization of these metrics that can impair their correct use. These pitfalls include the fact that different pain measures yield different MCIDs, that efficacy in clinical trials is impacted by various factors (population characteristics, trial design), that the MCID value is impacted by the method used to calculate it (anchor, distribution), by the type of anchor chosen and by the definition (threshold) of improvement. The MCID is also dependent on the population characteristics such as disease type and severity, sex, age, etc. For appropriate use, the MCID should be applied to changes in individual subjects, not to group changes. The MCID and CID are useful tools to define general guidelines to determine whether a treatment produces clinically meaningful effects. However, the many pitfalls associated with these metrics require a detailed understanding of the methods to calculate them and their context of use. Orthopedic surgeons that will use these metrics need to carefully understand them and be aware of their pitfalls.
Caspase-8, RIPK1, and RIPK3 Coordinately Regulate Retinoic Acid-Induced Cell Differentiation and Necroptosis (2017)

Abstract Caspase-8, which is essential for death receptor-mediated apoptosis, inhibits necroptosis by suppressing the function of RIPK1 and RIPK3 to activate MLKL. We show that knockdown of caspase-8 expression in embryoid bodies derived from ES cells markedly enhances retinoic acid (RA)-induced cell differentiation and necroptosis, both of which are dependent on Ripkl and Ripk3. RA treatment obviously enhanced the expression of RA-specific genes having a retinoic acid response element (RARE) to induce cell differentiation, and induced marked expression of RIPK1, RIPK3 and MLKL to stimulate necroptosis. Caspase-8 knockdown induced RA receptor (RAR) to form a complex with RIPK1 and RIPK3 in the nucleus, and RAR interacting with RIPK1 and RIPK3 showed much stronger binding activity to RARE than RAR without RIPK1 or RIPK3. In Caspase-8-deficient mouse embryos, expression of RA-specific genes was obviously enhanced. Thus, caspase-8, RIPK1, and RIPK3 regulate RA-induced cell differentiation and necroptosis both in vitro and in vivo.
Temperature dependence of the free-exciton transition energy in zinc oxide by photoluminescence excitation spectroscopy (2003)

Photoluminescence (PL) and photoluminescence excitation (PLE) spectroscopies are used to track the temperature dependence of the A exciton energy (EXA) in undoped bulk ZnO crystals grown by the seeded-chemical-vapor-transport method. For T&amp;gt;150 K, the edge emission becomes broad as the A exciton recombination and its longitudinal-optical (LO) phonon replica become superimposed. We use PLE to determine the temperature dependence of EXA by monitoring the broad green emission commonly observed in as-grown ZnO crystals, and thus have established the energy difference between the EXA and PL emission peak energies. The PL emission at 3.26 eV at room temperature is shown to be offset by about 50 meV to lower energy than the actual EXA transition. The temperature dependence of the energy difference between the EXA and PL peaks is compared with predictions based on the lineshape function for the EXA– LO recombination. At 300 K, the PL is predominantly composed of EXA– LO recombination. Further, the temperature dependence of the EXA transition energy can be described using standard expressions and the Debye and Einstein temperatures are found to be 700±30 and 240±5 K, respectively. The slope of the EXA versus T curve for ZnO approaches a constant value of dEXA/dT=−0.35 meV/K near room temperature.
Antinociceptive effect of sumatriptan in mice. (1998)

Antinociceptive effect of the antimigraine drug sumatriptan (5-HT1A agonist) was studied against acetic acid-induced writhing in mice. Sumatriptan produced the effect in a dose-dependent manner (1, 5, 10 and 20 mg/kg, s.c.). Naloxone (1 mg/kg i.p.) an opiate antagonist failed to reverse sumatriptan-induced antinociception. Cholinomimetic physostigmine (0.05 mg/kg, i.p.) potentiated and the muscarinic antagonist atropine (5 mg/kg, i.p.) blocked the antinociceptive effect of sumatriptan, respectively. The antinociceptive effect of sumatriptan was compared with an another 5-HT agonist (5-HT1A) buspirone which also produced antinociception. Like sumatriptan-analgesia, the buspirone response was also potentiated by physostigmine in atropine sensitive way. Further, buspirone potentiated the analgesic effect of sumatriptan. These observations suggest that 5-HT1A agonists produce antinociception possibly by modulating central cholinergic activity.
A Structural Model of Transcription Elongation (2000)

The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase (RNAP) and transcript RNA or template DNA onto the x-ray crystal structure. In the resulting model, the downstream duplex DNA is nestled in a trough formed by the beta' subunit and enclosed on top by the beta subunit. In the RNAP channel, the RNA/DNA hybrid extends from the enzyme active site, along a region of the beta subunit harboring rifampicin resistance mutations, to the beta' subunit "rudder." The single-stranded RNA is then extruded through another channel formed by the beta-subunit flap domain. The model provides insight into the functional properties of the transcription complex.
Clique Migration: Affinity Grouping of Virtual Machines for Inter-cloud Live Migration (2014)

Affinity is common among Virtual Machines (VMs) in cloud environments. If VMs collaborating on a job are split in geographically distributed clouds, the low bandwidth and high latency inter-cloud communication via a wide area network (WAN) will dramatically degrade the system performance. A potential solution is migrating all of the VMs collaborating on a job in parallel, so as to avoid wide area communication. However, if the job is too large, it becomes impractical to migrate all of the VMs simultaneously due to limited WAN bandwidth and high block dirty rate. We propose a migration optimization mechanism called Clique Migration to partition a large group of VMs into subgroups based on the traffic affinities among VMs. Then, subgroups are migrated one at a time. Based on Clique Migration, we propose and implement two algorithms called R-Min-Cut and Kmeans-SF. Analysis of the traffic trace of 68 VMs in an IBM production cluster shows that our algorithms can reduce inter-cloud traffic by 25% to 60%, when the degree of parallel migration is from 2 to 32. Tests of MPI multi-Ping Ping benchmark running on simulated inter-cloud environments, show that our algorithms can significantly shorten the period during which applications undergo performance degradation. Tests of MPI Reduce scatter benchmark show that R-Min-Cut can keep the performance during migration at 26% to 75% of the non-migration scenario.
Breast Conservation Therapy in Patients With Stage T1–T2 Breast Cancer (2010)

Use of breast-conserving surgical therapy should be optimized to enhance therapeutic outcome. Many developments in the oncological field and refinements in treatment planning and delivery of radiation therapy provide unique opportunities for the radiation oncologist to continue to play an integral role in the management of patients with breast cancer.
Loading-Induced Bone Formation is Mediated by Wnt1 Induction in Osteoblast-Lineage Cells (2022)

Abstract Mechanical loading on the skeleton stimulates bone formation. Although the exact mechanism underlying this process remains unknown, a growing body of evidence indicates that the Wnt signaling pathway is necessary for the skeletal response to loading. Recently, we showed that Wnts produced by osteoblast lineage cells mediate the osteo-anabolic response to tibial loading in adult mice. Here, we report that Wnt1 specifically plays a crucial role in mediating the mechano-adaptive response to loading. Independent of loading, short-term loss of Wnt1 in the Osx-lineage resulted in decreased cortical bone area in the tibias of 5-month old mice. In females, strain-matched loading enhanced periosteal bone formation in Wnt1F/F controls, but not in Wnt1F/F; OsxCreERT2 knockouts. In males, strain-matched loading increased periosteal bone formation in both control and knockout mice; however, the periosteal relative bone formation rate was 65% lower in Wnt1 knockouts versus controls. Together, these findings show that Wnt1 supports adult bone homeostasis and mediates the bone anabolic response to mechanical loading.
Iridium-Catalyzed Silylation of Aryl C–H Bonds (2014)

A method for the iridium-catalyzed silylation of aryl C-H bonds is described. The reaction of HSiMe(OSiMe3)2 with arenes and heteroarenes catalyzed by the combination of [Ir(cod)(OMe)]2 and 2,4,7-trimethylphenanthroline occurs with the aromatic compound as the limiting reagent and with high levels of sterically derived regioselectivity. This new catalytic system occurs with a much higher tolerance for functional groups than the previously reported rhodium-catalyzed silylation of aryl C-H bonds and occurs with a wide range of heteroarenes. The silylarene products are suitable for further transformations, such as oxidation, halogenation, and cross-coupling. Late-stage functionalization of complex pharmaceutical compounds was demonstrated.
Participation of the endoplasmic reticulum protein chaperone thio-oxidoreductase in gonadotropin-releasing hormone receptor expression at the plasma membrane (2009)

Chaperone members of the protein disulfide isomerase family can catalyze the thiol-disulfide exchange reaction with pairs of cysteines. There are 14 protein disulfide isomerase family members, but the ability to catalyze a thiol disulfide exchange reaction has not been demonstrated for all of them. Human endoplasmic reticulum protein chaperone thio-oxidoreductase (ERp18) shows partial oxidative activity as a protein disulfide isomerase. The aim of the present study was to evaluate the participation of ERp18 in gonadotropin-releasing hormone receptor (GnRHR) expression at the plasma membrane. Cos-7 cells were cultured, plated, and transfected with 25 ng (unless indicated) wild-type human GnRHR (hGnRHR) or mutant GnRHR (Cys14Ala and Cys200Ala) and pcDNA3.1 without insert (empty vector) or ERp18 cDNA (75 ng/well), pre-loaded for 18 h with 1 microCi myo-[2-3H(N)]-inositol in 0.25 mL DMEM and treated for 2 h with buserelin. We observed a decrease in maximal inositol phosphate (IP) production in response to buserelin in the cells co-transfected with hGnRHR, and a decrease from 20 to 75 ng of ERp18 compared with cells co-transfected with hGnRHR and empty vector. The decrease in maximal IP was proportional to the amount of ERp18 DNA over the range examined. Mutants (Cys14Ala and Cys200Ala) that could not form the Cys14-Cys200 bridge essential for plasma membrane routing of the hGnRHR did not modify maximal IP production when they were co-transfected with ERp18. These results suggest that ERp18 has a reduction role on disulfide bonds in wild-type hGnRHR folding.
An Inventive Method for Eco-Efficient Operation of Home Energy Management Systems (2018)

A demand response (DR) based home energy management systems (HEMS) synergies with renewable energy sources (RESs) and energy storage systems (ESSs). In this work, a three-step simulation based posteriori method is proposed to develop a scheme for eco-efficient operation of HEMS. The proposed method provides the trade-off between the net cost of energy ( C E n e t ) and the time-based discomfort ( T B D ) due to shifting of home appliances (HAs). At step-1, primary trade-offs for C E n e t , T B D and minimal emissions T E M i s s are generated through a heuristic method. This method takes into account photovoltaic availability, the state of charge, the related rates for the storage system, mixed shifting of HAs, inclining block rates, the sharing-based parallel operation of power sources, and selling of the renewable energy to the utility. The search has been driven through multi-objective genetic algorithm and Pareto based optimization. A filtration mechanism (based on the trends exhibited by T E M i s s in consideration of C E n e t and T B D ) is devised to harness the trade-offs with minimal emissions. At step-2, a constraint filter based on the average value of T E M i s s is used to filter out the trade-offs with extremely high values of T E M i s s . At step-3, another constraint filter (made up of an average surface fit for T E M i s s ) is applied to screen out the trade-offs with marginally high values of T E M i s s . The surface fit is developed using polynomial models for regression based on the least sum of squared errors. The selected solutions are classified for critical trade-off analysis to enable the consumer choice for the best options. Furthermore, simulations validate our proposed method in terms of aforementioned objectives.
The Arabidopsis homeobox gene SHOOT MERISTEMLESS has cellular and meristem‐organisational roles with differential requirements for cytokinin and CYCD3 activity (2013)

The Arabidopsis class-1 KNOX gene SHOOT MERISTEMLESS (STM) encodes a homeodomain transcription factor essential for shoot apical meristem (SAM) formation and sustained activity. STM activates cytokinin (CK) biosynthesis in the SAM, but the extent to which STM function is mediated through CK is unclear. Here we show that STM inhibits cellular differentiation and endoreduplication, acting through CK and the CK-inducible CYCD3 cell cycle regulators, establishing a mechanistic link to cell cycle control which provides sustained mitotic activity to maintain a pool of undifferentiated cells in the SAM. Equivalent functions are revealed for the related KNOX genes KNAT1/BP and KNAT2 through ectopic expression. STM is also required for proper meristem organisation and can induce de novo meristem formation when expressed ectopically, even when CK levels are reduced or CK signaling is impaired. This function in meristem establishment and organisation can be replaced by KNAT1/BP, but not KNAT2, despite its activation of CK responses, suggesting that promotion of CK responses alone is insufficient for SAM organisation. We propose that STM has dual cellular and meristem-organisational functions that are differentially represented in the class-1 KNOX gene family and have differing requirements for CK and CYCD3.
Co‐selection of cognate antibody‐antigen pairs by selectively‐infective phages (1995)

We have developed a chloramphenicol resistant derivative of fd phage with which cognate pairs of antibodies and antigens can be selected. The phage genome encodes a fusion of single-chain antibody to the C-terminal domain of gIIIp, rendering the phage non-infective. The antigen fused to the N-terminal domains of gIIIp is encoded in the same phage genome. Antigen and antibody fusion interact with each other in the periplasm of the phage-producing cell, restoring infectivity. This system has a very low background and will allow simultaneous randomisation of antibody and antigen.
Numerical computation of the Green′s function of a layered media with rough interfaces (2007)

Abstract A numerical method for the calculation of the Green's function related to a layered media containing rough interfaces is presented. The method is based on the assumption that the perturbations of the rough surfaces from planar ones are objects located at both sides of the planar boundaries. Such an approach allows one to formulate the problem as a scattering of cylindrical or spherical waves from buried bodies, which can be solved by means of MoM. The method is effective for surfaces having a localized and arbitrary roughness. This asymptotic behavior of the Green's function is also derived for large distances. The Green's function obtained here is applied to some direct and inverse scattering problems related to objects buried in a layered background to see its effectiveness and applicability. © 2007 Wiley Periodicals, Inc. Microwave Opt Technol Lett 49: 1204–1209, 2007; Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/mop.22401
Mineralization (2016)

Like most of the materials used by humans, polymeric materials are proposed in the literature and occasionally exploited clinically, as such, as devices or as part of devices, by surgeons, dentists, and pharmacists to treat traumata and diseases. Applications have in common the fact that polymers function in contact with animal and human cells, tissues, and/or organs. More recently, people have realized that polymers that are used as plastics in packaging, as colloidal suspension in paints, and under many other forms in the environment, are also in contact with living systems and raise problems related to sustainability, delivery of chemicals or pollutants, and elimination of wastes. These problems are basically comparable to those found in therapy. Last but not least, biotechnology and renewable resources are regarded as attractive sources of polymers. In all cases, water, ions, biopolymers, cells, and tissues are involved. Polymer scientists, therapists, biologists, and ecologists should thus use the same terminology to reflect similar properties, phenomena, and mechanisms. Of particular interest is the domain of the so-called “degradable or biodegradable polymers” that are aimed at providing materials with specific time-limited applications in medicine and in the environment where the respect of living systems, the elimination, and/or the bio-recycling are mandatory, at least ideally.