Miracle-dz/UniFAR-FTUs huggingface dataset:
Certifying Polynomials for AC 0 [ ⊕ ] Circuits , with Applications to Lower Bounds and Circuit Compression

In this paper, we study the method of certifying polynomials for proving AC0[⊕] circuit lower bounds. We use this method to show that Approximate Majority on n bits cannot be computed by AC0[⊕] circuits of size n1+o(1). This implies a separation between the power of AC0[⊕] circuits of near-linear size and uniform AC0[⊕] (and even AC0) circuits of polynomial size. This also implies a separation between randomized AC0[⊕] circuits of linear size and deterministic AC0[⊕] circuits of near-linear size. Our proof using certifying polynomials extends the deterministic restrictions technique of Chaudhuri and Radhakrishnan (STOC 1996), who showed that Approximate Majority cannot be computed by AC0 circuits of size n1+o(1). At the technical level, we show that for every AC0[⊕] circuit C of near-linear size, there is a low-degree polynomial P over F2 such that the restriction of C to the support of P is constant. Preliminary versions of this paper appeared in FSTTCS 2012 [19] and on ECCC [29]. ∗Supported in part by a Sloan Fellowship and NSF grant CCF-1253886. †Supported by DST Inspire grant IFA12-ENG14. Work partially done when the author was a postdoc at IAS, Princeton and DIMACS, Rutgers University. ACM Classification: F.1. 3 AMS Classification: 68Q17,68Q15
Attraction behaviour of Anagrus nilaparvatae to remote lemongrass (Cymbopogon distans) oil and its volatile compounds

Abstract Utilisation of Anagrus nilaparvatae is a promising and effective method for planthoppers manipulation. Twenty-seven components of remote lemongrass (Cymbopogon distans) oil were identified by GC/MS and nine volatiles were selected for behavioural experiments. In this study, we noted that the remote lemongrass oil was attractive to female A. nilaparvatae at concentrations of 0.1 and 1 mg/L. α-Pinene, β-pinene, eucalyptol, carveol and D-carvone attracted female wasps in the dose-dependent bioassays. Blend 1 (a mixture of eucalyptol, D-carvone, carveol, α-pinene, and β-pinene with ratios of remote lemongrass oil volatiles of 625:80:11:5:3) attracted female wasps at 10 mg/L, while blend 2 (a mixture of the same five volatiles at the same loading ratio) attracted them at 0.1 and 1 mg/L. These results suggested that plant essential oils could be attractants for natural enemies to control pests. The ratios of volatiles in the mixtures affect the attractiveness of the synthetic mixtures.
Dualsteric GPCR targeting: a novel route to binding and signaling pathway selectivity

Selective modulation of cell function by G protein‐coupled receptor (GPCR) activation is highly desirable for basic research and therapy but difficult to achieve. We present a novel strategy toward this goal using muscarinic acetylcholine receptors as a model. The five subtypes bind their physiological transmitter in the highly conserved orthosteric site within the transmembrane domains of the receptors. Orthosteric muscarinic activators have no binding selectivity and poor signaling specificity. There is a less well conserved allosteric site at the extracellular entrance of the binding pocket. To gain subtype‐selective receptor activation, we synthesized two hybrids fusing a highly potent oxotremorine‐like orthosteric activator with M2‐selective bis(ammonio)alkane‐type allosteric fragments. Radioligand binding in wild‐type and mutant receptors supplemented by receptor docking simulations proved M2 selective and true allosteric/orthosteric binding. G protein activation measurements using orthosteric and allosteric blockers identified the orthosteric part of the hybrid to engender receptor activation. Hybrid‐induced dynamic mass redistribution in CHO‐hM2 cells disclosed pathway‐specific signaling. Selective receptor activation (M2>M1>M3) was verified in living tissue preparations. As allosteric sites are increasingly recognized on GPCRs, the dualsteric concept of GPCR targeting represents a new avenue toward potent agonists for selective receptor and signaling pathway activation. — Antony, J., Kellershohn, K. , Mohr‐Andrä, M. , Kebig, A. , Prilla, S. , Muth, M. , Heller, E. , Disingrini, T. , Dallanoce, C. , Bertoni, S. , Schrobang, J., Tränkle, C. , Kostenis, E. , Christopoulos, A. , Höltje, H. ‐D. , Barocelli, E. , De Amici, M. , Holzgrabe, U. , Mohr, K. Dualsteric GPCR targeting: a novel route to binding and signaling pathway selectivity. FASEB J. 23, 442–450 (2009)
Disulfide cross-linking indicates that FlgM-bound and free σ28 adopt similar conformations

The dissociable σ subunit of bacterial RNA polymerase is required for the promoter-specific initiation of transcription. When bound to RNA polymerase, σ makes sequence-specific promoter contacts and plays a crucial role in DNA melting. In isolation, however, σ lacks significant promoter binding activity. In the crystal structure of the flagellar σ factor, σ28, bound to the anti-σ factor, FlgM, σ28 adopts a compact conformation in which the promoter binding surfaces are occluded by interdomain contacts. To test whether σ28 adopts this conformation in the absence of FlgM, we engineered a set of double cysteine mutants predicted to form interdomain disulfides in the conformation observed in the FlgM complex. We show that these disulfides form in both the presence and absence of FlgM. For two of the mutants, quantitative measurements of disulfide formation under equilibrium conditions suggest that the major solution conformation favors disulfide formation. The results indicate that the compact conformation of σ28 observed in the σ28/FlgM structure is similar to the predominant conformation of free σ28 in solution. This finding suggests that autoinhibition of DNA binding in free σ28 is accomplished by steric occlusion of the promoter binding surfaces by interdomain interactions within the σ factor as well as by a suboptimal distance between the promoter −10 and −35 element binding determinants in σ2 and σ4, respectively.
Adhesion Studies of Microorganisms on Natural Ore Material

In the course of the decline of high-grade ore deposits, new effective and eco-friendly bioleaching techniques are of interest. In-situ leaching is an auspicious method, but composition of leaching community should be adapted to the respective external conditions and the ore material. In this study several sulfidic minerals were inoculated into acidic mine water of a mine in eastern Germany, housing members of well-known iron oxidizing bacteria like Acidithiobacillus, Leptospirillum and Ferrovum. The attachment tests were performed in batch and in a continuous way at different temperatures. The analysis of the extracted DNA from adhered cells showed an enrichment of Ferrovum spp. on chalcopyrite surface under in-situ conditions at 11°C. For laboratory batch conditions an accumulation of Leptospirillum spp. was detected for adhered cells probably due to the changes of the physicochemical parameter of the mine water. In more detailed analyses we aim to elucidate possible preferential attachment of the mine water community members to certain minerals.
Temporal regularity facilitates higher‐order sensory predictions in fast auditory sequences

Does temporal regularity facilitate prediction in audition? To test this, we recorded human event‐related potentials to frequent standard tones and infrequent pitch deviant tones, pre‐attentively delivered within isochronous and anisochronous (20% onset jitter) rapid sequences. Deviant tones were repeated, either with high or low probability. Standard tone repetition sets a first‐order prediction, which is violated by deviant tone onset, leading to a first‐order prediction error response (Mismatch Negativity). The response to highly probable deviant repetitions is, however, attenuated relative to less probable repetitions, reflecting the formation of higher‐order sensory predictions. Results show that temporal regularity is required for higher‐order predictions, but does not modulate first‐order prediction error responses. Inverse solution analyses (Variable Resolution Electrical Tomography; VARETA) localized the error response attenuation to posterior regions of the left superior temporal gyrus. In a control experiment with a slower stimulus rate, we found no evidence for higher‐order predictions, and again no effect of temporal information on first‐order prediction error. We conclude that: (i) temporal regularity facilitates the establishing of higher‐order sensory predictions, i.e. ‘knowing what next’, in fast auditory sequences; (ii) first‐order prediction error relies predominantly on stimulus feature mismatch, reflecting the adaptive fit of fast deviance detection processes.
Municipal Solid Waste Collection and Management Problems: A Literature Review

This paper presents a review of the available literature on solid waste management problems, with a particular focus on vehicle routing problems. The available papers are classified into different categories with the purpose of providing the reader with a guide that facilitates his or her search for papers in his or her field of interest. For each category, a table is presented that gives a summary of how each paper scores from that perspective. Additional explanation is presented about the characteristics of each category using some key references. Finally, this paper discovers unexplored areas of research and identifies trends in the literature.
Population Dynamics in Heterogeneous Environments: a discrete Model

We study the dynamics of a multidimensional coordinate-dependent mapping governing the time evolution of a population spread over a one-dimensional lattice. The nonlinearity is of mean-field type and the dependence on coordinates, given by the so-called fitness, allows to take into account the spatial heterogeneities of the habitat. A global picture of the dynamics is given in the case without diffusion and in the case with diffusion when the fitness is homogeneous and leads to a periodic orbit. Moreover it is shown that, periodic fitnesses close to homogeneous ones impose their periodicity on the asymptotic dynamics when the latter is time-periodic.
Factors and Mechanisms for Pharmacokinetic Differences between Pediatric Population and Adults

Many physiologic differences between children and adults may result in age-related changes in pharmacokinetics and pharmacodynamics. Factors such as gastric pH and emptying time, intestinal transit time, immaturity of secretion and activity of bile and pancreatic fluid among other factors determine the oral bioavailability of pediatric and adult populations. Anatomical, physiological and biochemical characteristics in children also affect the bioavailability of other routes of administration. Key factors explaining differences in drug distribution between the pediatric population and adults are membrane permeability, plasma protein binding and total body water. As far as drug metabolism is concerned, important differences have been found in the pediatric population compared with adults both for phase I and phase II metabolic enzymes. Immaturity of glomerular filtration, renal tubular secretion and tubular reabsorption at birth and their maturation determine the different excretion of drugs in the pediatric population compared to adults.
Seeing the Forest or the Trees? Shifting Categorical Effects in Map Memory

Abstract People use spatial and nonspatial information to structure memory for an environment. Two experiments explored interactions between spatial and social categories on map memory when mediated by retrieval (Experiment 1) and encoding (Experiment 2) demands. Participants studied a map depicting business locations (including proprietors' race). In Experiment 1, participants completed two memory tasks, one globally focused and the other locally focused. The global task compressed, while the local task expanded, within-category similarity. Furthermore, processing styles carried over to the subsequent task. Experiment 2 emphasized either the spatial or social category during encoding, which increased that category's weighting in memory. These results extend the work of Maddox, Rapp, Brion, and Taylor, suggesting that retrieval and encoding demands can shift how these categories affect spatial memory.
Maternal and neonatal plasma microRNA biomarkers for fetal alcohol exposure in an ovine model.

BACKGROUND Plasma or circulating miRNAs (cir miRNAs) have potential diagnostic value as biomarkers for a range of diseases. Based on observations that ethanol (EtOH) altered intracellular miRNAs during development, we tested the hypothesis that plasma miRNAs were biomarkers for maternal alcohol exposure, and for past in utero exposure, in the neonate. METHODS Pregnant sheep were exposed to a binge model of EtOH consumption resulting in an average peak blood alcohol content of 243 mg/dl, for a third-trimester-equivalent period from gestational day 4 (GD4) to GD132. MiRNA profiles were assessed by quantitative PCR analysis in plasma, erythrocyte, and leukocytes obtained from nonpregnant ewes, and plasma from pregnant ewes 24 hours following the last binge EtOH episode, and from newborn lambs, at birth on ~GD147. RESULTS Pregnant ewe and newborn lamb cir miRNA profiles were similar to each other and different from nonpregnant female plasma, erythrocyte, or leukocyte miRNAs. Significant changes in cir miRNA profiles were observed in the EtOH-exposed ewe and, at birth, in the in utero, EtOH-exposed lamb. Cir miRNAs including miR-9, -15b, -19b, and -20a were sensitive and specific measures of EtOH exposure in both pregnant ewe and newborn lamb. Additionally, EtOH exposure altered guide-to-passenger strand cir miRNA ratios in the pregnant ewe, but not in the lamb. CONCLUSIONS Shared profiles between pregnant dam and neonate suggest possible maternal-fetal miRNA transfer. Cir miRNAs are biomarkers for alcohol exposure during pregnancy, in both mother and neonate, and may constitute an important shared endocrine biomarker that is vulnerable to the maternal environment.
Identification of the metabolites after oral administration of extract of ziziphi spinosae semen to rats or dogs by high-performance liquid chromatography/linear ion trap FTICR hybrid mass spectrometry.

Ziziphi spinosae semen (ZSS) is a traditional Chinese medicine that has been widely used to treat insomnia and anxiety. Modern pharmacological studies have demonstrated that flavonoids are the main active compounds in ZSS. However, the metabolites and the metabolic pathways of flavonoids in ZSS have not been investigated thoroughly. In this study, a method based on high-performance liquid chromatography coupled with Fourier transform ion cyclotron resonance mass spectrometry (HPLC/FTICR-MS) was established to identify the metabolites of flavonoids after oral administration of extract of ZSS to rats or dogs, using parent mass list-triggered data-dependent multiple-stage mass analysis at a resolving power of 50,000 in the external calibration mode. The mass accuracies obtained for all full-scan analyses were less than 4 ppm (<2 ppm in most cases). A total of 15 compounds were detected in biological samples of rats and dogs, and nine compounds were identified. The metabolic pathways of flavonoids of ZSS in rats and dogs were proposed. The results may help better understand the material basis and pharmacological mechanism of ZSS.
Tunable integrated optical modulator with dynamical photonic band transition of photonic crystals

A Mach-Zehnder Interferometer based optical modulator composed of photonic crystals as phase shifters is presented. The switching process relies on the phase modulation along the arms of interferometer resulted from the photonic band shift of the photonic crystal regions. A small bulk index change leads to a large effective index difference between two arms of the interferometer and a small foot-print device can operate as a modulator. Presented MZI-based optical modulator is shown to have tunable bandwidth up to 15.7nm. This interesting approach provides possibility of broadband, low-voltage, low-loss, high-speed and tunable optical integrated switches, modulators and multiplexers.
Effects of ACL reconstruction surgery on muscle activity of the lower limb during a jump‐cut maneuver in males and females

We compared muscle activity of the quadriceps, hamstring, and gastrocnemius muscles when ACL‐intact (ACLINT) and ACL‐reconstructed (ACLREC) male and female subjects performed a jump‐cut task. Surface electromyography sensors were used to evaluate time to peak muscle activity and muscle activity ratios. Rectus femoris (RF) and vastus medialis (VM) peak timing was 71 and 78 ms earlier in ACLINT than in ACLREC subjects, respectively. Biceps femoris (BF) peak timing was 90 ms earlier in ACLINT than in ACLREC subjects and 75 ms earlier in females than in males. Medial gastrocnemius (MG) muscle peak timing was 77 ms earlier in ACLINT than in ACLREC subjects. Lateral gastrocnemius (LG) and MG muscle peak times were 106 ms and 87 ms earlier in females than in males, respectively. The RF, VM, BF, and MG peaked later in ACLREC than in ACLINT subjects. There was evidence suggesting that the loading phase quadriceps:hamstring (quad:ham) muscle activity ratio was greater in ACLREC than in ACLINT subjects. Finally, the injury risk phase quad:ham muscle activity ratio was 4.8 times greater in females than in males. In conclusion, differences exist in muscle activity related to ACL status and sex that could potentially help explain graft failure risk and the sex bias. © 2013 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. Published by Wiley Periodicals, Inc. J Orthop Res 31:1890–1896, 2013
An Updated Review on Cancer Risk Associated with Incretin Mimetics and Enhancers

Incretin-based therapies, including the use of incretin mimetics of glucagon-like peptide-1 receptor (GLP-1R) agonists and incretin enhancers of dipeptidyl-peptidase 4 (DPP-4) inhibitors, are widely used by clinicians for glucose lowering in patients with type 2 diabetes mellitus. These agents have benefits of a lower risk of hypoglycemia, being neutral for body weight for DPP-4 inhibitors and having a potential for weight reduction with GLP-1R agonists. They may also have a neutral or beneficial cardiovascular effect. Despite these benefits, an increased risk of cancer (especially pancreatic cancer and thyroid cancer) associated with incretin-based therapies has been reported. In this article, we reviewed related literature of experimental animal and observational human studies, clinical trials, and meta-analyses published until December 15, 2014. Current studies suggested a probable role of GLP-1R activation on the development of pancreatic cancer and thyroid cancer in rodents, but such an effect in humans is not remarkable due to the lower or lack of expression of GLP-1R on human pancreatic ductal cells and thyroid tissues. Findings in human studies are controversial and inconclusive. In the analyses of the US Food and Drug Administration adverse events reporting system, a significantly higher risk of pancreatic cancer was observed for GLP-1R agonists and DPP-4 inhibitors, but a significantly higher risk of thyroid cancer was only observed for GLP-1R agonists. Such a higher risk of pancreatic cancer or thyroid cancer could not be similarly demonstrated in other human observational studies or analyses of data from clinical trials. With regards to cancers other than pancreatic cancer and thyroid cancer, available studies supported a neutral association in humans. Some preliminary studies even suggested a potentially beneficial effect on the development of other cancers with the use of incretins. Based on current evidence, continuous monitoring of the cancer issues related to incretin-based therapies is required, even though the benefits may outweigh the potential cancer risk in the general patients with type 2 diabetes mellitus.
Mutations in the Capsid Protein of Brome Mosaic Virus Affecting Encapsidation Eliminate Vesicle Induction In Planta: Implications for Virus Cell-to-Cell Spread

ABSTRACT Positive-strand RNA viruses are known to rearrange the endomembrane network to make it more conducive for replication, maturation, or egress. Our previous transmission electron microscopic (TEM) analysis showed that ectopic expression of wild-type (wt) capsid protein (CP) of Brome mosaic virus (BMV) has an intrinsic property of modifying the endoplasmic reticulum (ER) to induce vesicles similar to those present in wt BMV infection. In this study, we evaluated the functional significance of CP-mediated vesicle induction to the BMV infection cycle in planta. Consequently, the cytopathologic changes induced by wt CP or its mutants defective in virion assembly due to mutations engineered in either N- or C-proximal domains were comparatively analyzed by TEM in two susceptible (Nicotiana benthamiana and Chenopodium quinoa) and one nonhost (N. clevelandii) plant species. The results showed that in susceptible hosts, CP-mediated ER-derived vesicle induction is contingent on the expression of encapsidation-competent CP. In contrast, unlike in N. benthamiana and C. quinoa, transient expression of wt CP in nonhost N. clevelandii plants eliminated vesicle induction. Additionally, comparative source-to-sink analysis of virus spread in leaves of N. benthamiana and N. clevelandii coexpressing wt BMV and Cucumber mosaic virus (CMV) showed that despite trans-encapsidation, CMV failed to complement the defective cell-to-cell movement of BMV. The significance and relation of CP-mediated vesicle induction to virus cell-to-cell movement are discussed.
Lymphoproliferative response to herpes simplex virus type 1, cytomegalovirus, Epstein–Barr virus, varicella zoster virus, human herpes virus 6, 7, and 8 antigen stimulation in pediatric allogeneic stem cell transplant recipients

Cheng FWT, Chan PKS, Lee V, Leung WK, Shing MK, Li CK, Leung TF. Lymphoproliferative response to herpes simplex virus type 1, cytomegalovirus, Epstein‐Barr virus, varicella zoster virus, human herpes virus 6, 7, and 8 antigen stimulation in pediatric allogeneic stem cell transplant recipients. Pediatr Transplantation 2010: 14:761–769. © 2010 John Wiley & Sons A/S.
Design of fault-tolerant and dynamically-reconfigurable microfluidic biochips

Microfluidics-based biochips are soon expected to revolutionize clinical diagnosis, DNA sequencing, and other laboratory procedures involving molecular biology. Most microfluidic biochips are based on the principle of continuous fluid flow and they rely on permanently-etched microchannels, micropumps, and microvalves. We focus here on the automated design of "digital" droplet-based microfluidic biochips. In contrast to continuous-flow systems, digital microfluidics offers dynamic reconfigurability; groups of cells in a microfluidics array can be reconfigured to change their functionality during the concurrent execution of a set of bioassays. We present a simulated annealing-based technique for module placement in such biochips. The placement procedure not only addresses chip area, but it also considers fault tolerance, which allows a microfluidic module to be relocated elsewhere in the system when a single cell is detected to be faulty. Simulation results are presented for a case study involving the polymerase chain reaction.