Miracle-dz/UniFAR-FTUs huggingface dataset:
Fundamental processes of refractive index modifications during femtosecond laser waveguide writing

By using focused ultrashort pulsed laser radiation refractive index modifications are induced in glass in order to generate optical components. The understanding of physically fundamental processes induced by laser radiation is the basis for the systematic control and maximization of the refractive index change for the realization of three-dimensional, optical components for integrated optics like in-volume waveguides. In this paper fundamental processes which are induced by focused laser radiation in the volume of borosilicate glass D263 and fused silica are investigated. The glass materials are structured by laser radiation in the infrared spectral range (λ=1045nm). By using femtosecond laser pulses with high repetition rates (f = 500 kHz), thermal processes like heat accumulation effects are induced leading to heat affected zones and thus waveguide cross sections with dimensions larger than the focal spot. The absorptivity during modification in relation to the applied pulse energy is measured for different repetition rates in both glass materials. Furthermore, the laser induced structural change in the glass matrix by the increase of three- and four-membered ring structures is proved with Raman spectroscopy.
Herding Among Investment Newsletters: Theory and Evidence

A model is developed that implies that if an analyst has high reputation or low ability, or if there is strong public information that is inconsistent with the analyst's private information, she is likely to herd. Herding is also common when informative private signals are positively correlated across analysts. The model is tested using data from analysts who publish investment newsletters. Consistent with the model's implications, the empirical results indicate that a newsletter analyst is likely to herd on Value Line's recommendation if her reputation is high, if her ability is low, or if signal correlation is high. Recommendations are made about how to test herding models. Hard Copy Paper requests: Carol Bass at ceb4@mail.duke. edu, ask for working paper 9714.
Is Type 2 Diabetes an Operable Intestinal Disease?

Type 2 diabetes, which accounts for 90–95% of all cases of diabetes, is a growing epidemic that places a severe burden on health care systems, especially in developing countries. Because of both the scale of the problem and the current epidemic growth of diabetes, it is a priority to find new approaches to better understand and treat this disease. Gastrointestinal surgery may provide new opportunities in the fight against diabetes. Conventional gastrointestinal operations for morbid obesity have been shown to dramatically improve type 2 diabetes, resulting in normal blood glucose and glycosylated hemoglobin levels, with discontinuation of all diabetes-related medications. Return to euglycemia and normal insulin levels are observed within days after surgery, suggesting that weight loss alone cannot entirely explain why surgery improves diabetes. Recent experimental studies point toward the rearrangement of gastrointestinal anatomy as a primary mediator of the surgical control of diabetes, suggesting a role of the small bowel in the pathophysiology of the disease. This article presents available evidence in support of the hypothesis that type 2 diabetes may be an operable disease characterized by a component of intestinal dysfunction.
Finite Mobility Effects on the Radiative Efficiency Limit of Pn-Junction Solar Cells

The maximum power conversion efficiency of a solar cell as defined by the Shockley-Queisser (SQ) radiative recombination limit relies on the assumption that the collection probability for all photogenerated electron/hole-pairs is unity. This assumption implies a virtually infinite mobility mu of the photogenerated charge carriers. In order to compute the radiative efficiency limit with finite mobility, we solve the continuity equation for minority carriers including an additional integral term that accounts for emission of photons by radiative recombination and their subsequent reabsorption. Even when assuming radiative recombination as the only recombination mechanism, the achievable efficiency is reduced drastically when mu drops below a critical value muc. This critical value depends on the absorption coefficient and the doping density of the semiconductor. Thus, we give a criterion that has to be fulfilled by any photovoltaic material in order to guarantee charge separation even in an otherwise most ideal case. Finally, we extend our theory to finite non-radiative lifetimes thereby spanning the gap between the SQ theory and the classical textbook description of a pn-junction solar cell
Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry

An important problem in computational biology is predicting the structure of the large number of putative proteins discovered by genome sequencing projects. Fold‐recognition methods attempt to solve the problem by relating the target proteins to known structures, searching for template proteins homologous to the target. Remote homologs that may have significant structural similarity are often not detectable by sequence similarities alone. To address this, we incorporated predicted local structure, a generalization of secondary structure, into two‐track profile hidden Markov models (HMMs). We did not rely on a simple helix‐strand‐coil definition of secondary structure, but experimented with a variety of local structure descriptions, following a principled protocol to establish which descriptions are most useful for improving fold recognition and alignment quality. On a test set of 1298 nonhomologous proteins, HMMs incorporating a 3‐letter STRIDE alphabet improved fold recognition accuracy by 15% over amino‐acid‐only HMMs and 23% over PSI‐BLAST, measured by ROC‐65 numbers. We compared two‐track HMMs to amino‐acid‐only HMMs on a difficult alignment test set of 200 protein pairs (structurally similar with 3–24% sequence identity). HMMs with a 6‐letter STRIDE secondary track improved alignment quality by 62%, relative to DALI structural alignments, while HMMs with an STR track (an expanded DSSP alphabet that subdivides strands into six states) improved by 40% relative to CE. Proteins 2003;51:504–514. © 2003 Wiley‐Liss, Inc.
Non-Iterative, Robust Monte Carlo Noise Reduction

A novel Monte Carlo noise reduction operator is proposed in this paper. We apply and extend the standard bilateral filtering method and build a new local adaptive noise reduction kernel. It first computes the initial estimate of each pixel, and then applies bilateral filtering using this initial estimate in its range filtering kernel. It is simple both in formulation and implementation. The new operator is robust and fast in the sense that it can suppress the outliers, as well as the inter-pixel incoherence in a non-iterative way. It can be easily integrated into existing rendering systems, and such a framework is shown in this paper. The results of our approach are compared with those of other methods. A GPU implementation of our algorithm runs in 500ms for a 512×512 image.
Treatment of Atrial Fibrillation With Antiarrhythmic Drugs or Radiofrequency Ablation: Two Systematic Literature Reviews and Meta-Analyses

Background—Although radiofrequency catheter ablation (RFA) has evolved from an experimental procedure to an important treatment option for atrial fibrillation, the relative safety and efficacy of catheter ablation relative to that of antiarrhythmic drug (AAD) therapy has not been established. Methods and Results—Two separate systematic reviews were conducted: one on RFA and the other on AAD to provide accurate and broadly representative estimates of the clinical efficacy and safety of both therapies in the treatment of atrial fibrillation. Electronic searches were conducted in EMBASE and MEDLINE from 1990 to 2007. For the RFA review, all study designs were accepted. For the AAD review, articles were limited to prospective studies on the following drugs of interest: amiodarone, dofetilide, sotalol, flecainide, and propafenone. Data were extracted by 1 reviewer, with a second reviewer performing independent confirmation of extracted data. Sixty-three RFA and 34 AAD studies were included in the reviews. Patients enrolled in RFA studies tended to be younger (mean age, 55 versus 62 years), had longer duration of atrial fibrillation (6.0 versus 3.1 years), and had failed a greater number of prior drug trials (2.6 versus 1.7). The single-procedure success rate of ablation off AAD therapy was 57% (95% CI, 50% to 64%), the multiple procedure success rate off AAD was 71% (95% CI, 65% to 77%), and the multiple procedure success rate on AAD or with unknown AAD usage was 77% (95% CI, 73% to 81%). In comparison, the success rate for AAD therapy was 52% (95% CI, 47% to 57%). A major complication of catheter ablation occurred in 4.9% of patients. Adverse events for AAD studies, although more common (30% versus 5%), were less severe. Conclusions—Studies of RFA for treatment of atrial fibrillation report higher efficacy rates than do studies of AAD therapy and a lower rate of complications.
Phospholipase D1 Mediates AMP-Activated Protein Kinase Signaling for Glucose Uptake

Background Glucose homeostasis is maintained by a balance between hepatic glucose production and peripheral glucose utilization. In skeletal muscle cells, glucose utilization is primarily regulated by glucose uptake. Deprivation of cellular energy induces the activation of regulatory proteins and thus glucose uptake. AMP-activated protein kinase (AMPK) is known to play a significant role in the regulation of energy balances. However, the mechanisms related to the AMPK-mediated control of glucose uptake have yet to be elucidated. Methodology/Principal Findings Here, we found that AMPK-induced phospholipase D1 (PLD1) activation is required for 14C-glucose uptake in muscle cells under glucose deprivation conditions. PLD1 activity rather than PLD2 activity is significantly enhanced by glucose deprivation. AMPK-wild type (WT) stimulates PLD activity, while AMPK-dominant negative (DN) inhibits it. AMPK regulates PLD1 activity through phosphorylation of the Ser-505 and this phosphorylation is increased by the presence of AMP. Furthermore, PLD1-S505Q, a phosphorylation-deficient mutant, shows no changes in activity in response to glucose deprivation and does not show a significant increase in 14C-glucose uptake when compared to PLD1-WT. Taken together, these results suggest that phosphorylation of PLD1 is important for the regulation of 14C-glucose uptake. In addition, extracellular signal-regulated kinase (ERK) is stimulated by AMPK-induced PLD1 activation through the formation of phosphatidic acid (PA), which is a product of PLD. An ERK pharmacological inhibitor, PD98059, and the PLD inhibitor, 1-BtOH, both attenuate 14C-glucose uptake in muscle cells. Finally, the extracellular stresses caused by glucose deprivation or aminoimidazole carboxamide ribonucleotide (AICAR; AMPK activator) regulate 14C-glucose uptake and cell surface glucose transport (GLUT) 4 through ERK stimulation by AMPK-mediated PLD1 activation. Conclusions/Significance These results suggest that AMPK-mediated PLD1 activation is required for 14C-glucose uptake through ERK stimulation. We propose that the AMPK-mediated PLD1 pathway may provide crucial clues to understanding the mechanisms involved in glucose uptake.
A Vector-Sum Theorem and its Application to Improving Flow Shop Guarantees

We prove that if a closed polygonal path in Rd consists of a finite number of line segments of at most unit length, then it is possible to transpose the segments in such a way that the new polygonal path is contained in a ball of radius [ $\frac{3}{2}d$ ]. Using this result we give a near optimal algorithm for the NP-complete flow shop problem. The error of the algorithm cannot exceed a constant depending on the maximal execution time and the number of machines but not depending on the number of jobs. Our theorems improve earlier results of the same type by Belov and Stolin.
Chromosomal position mediates spinal cord expression of a dbx1a enhancer

Dbx homeodomain proteins are important for the production of multiple spinal cord cell types. To examine the regulation of Dbx genes in more detail, we have generated transgenic zebrafish in which fluorescent protein expression is driven by predicted dbx1a enhancers. We identified three areas of sequence conservation upstream of the dbx1a coding sequence and generated fluorescent reporter constructs driven by these predicted enhancer elements and the endogenous dbx1a promoter. In multiple stable insertions of a 3.5‐kb enhancer fragment, we observed that there was additional reporter expression in the dorsal spinal cord not normally observed by dbx1a in situ hybridization. In addition, these lines exhibited only transient reporter expression, unlike the endogenous gene. Surprisingly, a single insertion line expressed the reporter in the endogenous pattern, indicating that other local regulatory elements modulate gene expression through the 3.5‐kb enhancer. Developmental Dynamics 238:2929–2935, 2009. © 2009 Wiley‐Liss, Inc.
An energy minimization algorithm for cooperative spectrum sensing

We introduce an algorithm minimizing the consumed energy of a cooperative spectrum sensing-based cognitive radio network. The energy is minimized, while satisfying requirements for primary user protection and for secondary user data rate simultaneously, with respect to the powers for transmitting on control and data channels, the number of reported bits, and the thresholds of the global sensing test. Control and data channels are assumed not to be error-free. Simulation results finally confirm our claims.
Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

Significance The study of ecological succession remains at the core of ecology. Understanding the trajectories and mechanisms controlling ecological succession is crucial to predicting the responses of ecosystems to environmental change and projecting their future states. By definition, deterministic succession is expected under homogeneous abiotic and biotic starting conditions. This study, however, shows that the succession of groundwater microbial communities in response to nutrient amendment is primarily stochastic, but that the drivers controlling biodiversity and succession are dynamic rather than static. By identifying the mechanisms controlling microbial community assembly and succession, this study makes fundamental contribution to the mechanistic understanding essential for a predictive microbial ecology of many systems ranging from microbiomes of humans and plants to natural and managed ecosystems. Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession.
Study of Electrical and Optical Properties of Zr-Doped ZnO Thin Films Prepared by DC Reactive Magnetron Sputtering

This paper establishes DC reactive magnetron sputtering as synthesis process for Zr doped ZnO thin film. Zr can be doped in ZnO using various techniques. Some research groups have doped ZnO with Zr by radio frequency magnetron sputtering using target made of ZnO and ZrO2 powder. Radio frequency has low rate of deposition because deposition takes place only in one of two half cycles. Uniform mixing of small amount of ZrO2 powder in ZnO is expensive process as well as time consuming. To overcome the constraints, Zn and Zr metal target was used and film was made by DC reactive magnetron sputtering. Various parameters of the process was established by varying variables, such as sputtering power of the Zn and Zr, oxygen partial pressure in the chamber. Optimum flow rate of Argon is 16 sccm and Oxygen is 4 sccm. Sputtering power of 150 watt for Zn and 10 watt for the Zr gives good result. Films obtained are polycrystalline with a hexagonal structure and have preferred orientation along the c axis. Resistivity of the film is as low as 0.07 Ω-cm. Average transparency of film is above 85% in visible range.
Influence of Substrate Mineralogy on Bacterial Mineralization of Calcium Carbonate: Implications for Stone Conservation

ABSTRACT The influence of mineral substrate composition and structure on bacterial calcium carbonate productivity and polymorph selection was studied. Bacterial calcium carbonate precipitation occurred on calcitic (Iceland spar single crystals, marble, and porous limestone) and silicate (glass coverslips, porous sintered glass, and quartz sandstone) substrates following culturing in liquid medium (M-3P) inoculated with different types of bacteria (Myxococcus xanthus, Brevundimonas diminuta, and a carbonatogenic bacterial community isolated from porous calcarenite stone in a historical building) and direct application of sterile M-3P medium to limestone and sandstone with their own bacterial communities. Field emission scanning electron microscopy (FESEM), atomic force microscopy (AFM), powder X-ray diffraction (XRD), and 2-dimensional XRD (2D-XRD) analyses revealed that abundant highly oriented calcite crystals formed homoepitaxially on the calcitic substrates, irrespective of the bacterial type. Conversely, scattered spheroidal vaterite entombing bacterial cells formed on the silicate substrates. These results show that carbonate phase selection is not strain specific and that under equal culture conditions, the substrate type is the overruling factor for calcium carbonate polymorph selection. Furthermore, carbonate productivity is strongly dependent on the mineralogy of the substrate. Calcitic substrates offer a higher affinity for bacterial attachment than silicate substrates, thereby fostering bacterial growth and metabolic activity, resulting in higher production of calcium carbonate cement. Bacterial calcite grows coherently over the calcitic substrate and is therefore more chemically and mechanically stable than metastable vaterite, which formed incoherently on the silicate substrates. The implications of these results for technological applications of bacterial carbonatogenesis, including building stone conservation, are discussed.
Machine learning methods in chemoinformatics

Machine learning algorithms are generally developed in computer science or adjacent disciplines and find their way into chemical modeling by a process of diffusion. Though particular machine learning methods are popular in chemoinformatics and quantitative structure–activity relationships (QSAR), many others exist in the technical literature. This discussion is methods‐based and focused on some algorithms that chemoinformatics researchers frequently use. It makes no claim to be exhaustive. We concentrate on methods for supervised learning, predicting the unknown property values of a test set of instances, usually molecules, based on the known values for a training set. Particularly relevant approaches include Artificial Neural Networks, Random Forest, Support Vector Machine, k‐Nearest Neighbors and naïve Bayes classifiers. WIREs Comput Mol Sci 2014, 4:468–481.
Read Consistency in Distributed Database Based on DMVCC

In a traditional distributed database system, the partitions use two-phase locking (2PL) as the concurrency control protocol to ensure distributed read consistency. But the read-lock acquired by a read operation is incompatible with a write-lock, which undermines the performance of the system. While in a system at the snapshot isolation level, where partitions use Multi-Version Concurrent Control (MVCC) as the concurrent control protocol, distributed read inconsistency may occur. To achieve read consistency and guarantee the performance at the same time, we propose Distributed Multi-Version Concurrent Control (DMVCC). With DMVCC, the system can support snapshot reads, which do not block write operations, and ensure distributed read consistency. In this protocol, a transaction obtains a set of consistent snapshot version numbers at the startup time. The transaction then uses those numbers to read the corresponding data stored on each partition. The correctness of the protocol is strictly proved. We conduct a series of experiments to compare the performance of the system when using and not using DMVCC with a scaled TPC-C benchmark. We observe that our DMVCC based system outperforms the system using 2PL at both medium (up to 1.53x speed up) and high contention (up to 2.0x speed up) levels. Furthermore, when read/write ratio goes up to 1:1, the throughput of the DMVCC based system is 290% higher than that of the system using 2PL. The scalability of the system is also presented.
Neoadjuvant Chemotherapy for Breast Cancer

Neoadjuvant chemotherapy (NAC), also termed as preoperative, induction or primary che‐ motherapy, is defined as the administration of systemic chemotherapeutic agent prior to lo‐ cal control of surgery or radiation. Giving chemotherapy before performing a resection of tumour was initially introduced in locally advanced breast cancer where large inoperable tumour can be converted to operable cancer.
Ca 2 + influx is required for extended synaptotagmin 1-induced ER-plasma membrane tethering

The extended synaptotagmins (E-Syts) are ER proteins that act as Ca-regulated tethers between the ER and the plasma membrane (PM) and have a putative role in lipid transport between the two membranes. Ca regulation of their tethering function, as well as the interplay of their different domains in such function, remains poorly understood. By exposing semi-intact cells to buffers of variable Ca concentrations, we found that binding of E-Syt1 to the PI(4,5)P2-rich PM critically requires its C2C and C2E domains and that the EC50 of such binding is in the low micromolar Ca 2+ range. Accordingly, E-Syt1 accumulation at ER-PM contact sites occurred only upon experimental manipulations known to achieve these levels of Ca via its influx from the extracellular medium, such as store-operated Ca entry in fibroblasts and membrane depolarization in b-cells. We also show that in spite of their very different physiological functions, membrane tethering by E-Syt1 (ER to PM) and by synaptotagmin (secretory vesicles to PM) undergo a similar regulation by plasma membrane lipids and cytosolic Ca.