Miracle-dz/UniFAR-FTUs huggingface dataset:
Discrimination of Transgenic and Conventional Soybean Seeds by Fourier Transform Infrared Photoacoustic Spectroscopy

polymers and solutes, which leads to a strong partitioning effect, would actually slow down the diffusion process. The attraction force between the solution and the matrix becomes the molecular friction for the diffusion. Furthermore, those molecules that partition in the hair are larger than acetonitrile and 1-pentanenitrile. The size of the molecule could also contribute to the effect on the speed of diffusion as well as the molecular structure, like the difference between aliphatic hydrocarbons versus aromatic hydrocarbons. This brief study has illustrated the potential of this novel approach to investigate diffusion of solutes into micro fibers, such as human hair, in situ. The system could be further optimized by noting that a large area of the image was redundant in the analysis. A smaller FPA detector (e.g., a 32 3 32 array) would have collected the same information for a much shorter measurement time, and hence, a better temporal resolution. On the other hand, the large area measured could have been utilized for high throughput measurements by arranging several cross-sections of hair in the image field of view. Diffusion studies of different hair types or simply a larger number of repeat measurements can be carried out in parallel. Nevertheless, the idea of using this approach to study the diffusion of solutes in hair has been demonstrated. In summary, we have demonstrated the potential of in situ FT-IR spectroscopic imaging to study the diffusion of chemicals across the hair cross-section. All spectra were measured simultaneously, enabling the study of dynamic systems. The study of the diffusion of four model chemicals, acetonitrile, 1-pentanenitrile, 4-cyanophenol, and 4-cyanobenzoic acid, into hair cross-sections has been demonstrated. 4Cyanophenol and 4-cyanobenzoic acid require a much longer time to complete the diffusion process owing to their relatively larger molecular sizes and the possibility of the formation of Hbonds with the polar groups of the hair proteins. It is possible to further optimize this study by using a smaller FPA array for a better temporal resolution or arranging more hair crosssections into the field of view of the detector for high throughput studies. The demonstrated in situ approach can be applied to a wide range of diffusion studies, not limited to hair cross-sections but applicable to any biological tissues.
Postoperative Albumin Drop Is a Marker for Surgical Stress and a Predictor for Clinical Outcome: A Pilot Study

Background. Surgical stress during major surgery may be related to adverse clinical outcomes and early quantification of stress response would be useful to allow prompt interventions. The aim of this study was to evaluate the acute phase protein albumin in the context of the postoperative stress response. Methods. This prospective pilot study included 70 patients undergoing frequent abdominal procedures of different magnitude. Albumin (Alb) and C-reactive protein (CRP) levels were measured once daily starting the day before surgery until postoperative day (POD) 5. Maximal Alb decrease (Alb Δ min) was correlated with clinical parameters of surgical stress, postoperative complications, and length of stay. Results. Albumin values dropped immediately after surgery by about 10 g/L (42.2 ± 4.5 g/L preoperatively versus 33.8 ± 5.3 g/L at day 1, P < 0.001). Alb Δ min was correlated with operation length (Pearson ρ = 0.470, P < 0.001), estimated blood loss (ρ = 0.605, P < 0.001), and maximal CRP values (ρ = 0.391, P = 0.002). Alb Δ min levels were significantly higher in patients having complications (10.0 ± 5.4 versus 6.1 ± 5.2, P = 0.005) and a longer hospital stay (ρ = 0.285, P < 0.020). Conclusion. Early postoperative albumin drop appeared to reflect the magnitude of surgical trauma and was correlated with adverse clinical outcomes. Its promising role as early marker for stress response deserves further prospective evaluation.
Partial Evaluation of the Euclidian Algorithm (extended version)

Some programs are easily amenable to partial evaluation because their control flow clearly depends on one of their parameters. Specializing such programs with respect to this parameter eliminates the associated interpretive overhead. Some other programs, however, do not exhibit this interpreter-like behavior. Each of them presents a challenge for partial evaluation. The Euclidian algorithm is one of them, and in this article, we make it amenable to partial evaluation. We observe that the number of iterations in the Euclidian algorithm is bounded by a number that can be computed given either of the two arguments. We thus rephrase this algorithm using bounded recursion. The resulting program is better suited for automatic unfolding and thus for partial evaluation. Its specialization is efficient. Keywords: partial evaluation, scientific computation.
Computational schemes for biomimetic sculpture

A prototype system for the automatic evolution of biomimetic structures using structural automata is described and its utility for generating digital sculpture is demonstrated. Sculptures are generated from a primordial shape which is represented in terms of a triangular mesh and sculpture is created by extending the original surface using tetrahedral structural elements. Recursively applicable rules or equivalently, automata, are defined which allow the sculptor to generate a volumetric scaffold from the original surface. This scaffold is generated using the stated rules for inserting and connecting together the tetrahedral elements. The software is operated as a generative process where sculptures are grown from an original triangular surface mesh as a sequence of layers. Each layer is created as a 2-step process. In step 1, we populate the surface with tetrahedral structures where the base of each tetrahedron coincides with a surface triangle. Step 2 re-triangulates the apexes of the tetrahedra from step 1 creating an offset and deformed version of the original surface mesh. The sculptor has artistic control of the process at all points and may assign or change rules to generate different biomimetic behaviors, i.e., structures which tend to replicate natural phenomena.
Out-band interference rejection in UWB LNA receiver using coupled inductors in 3.1–10.6 GHz

In this paper, a UWB LNA circuit with a new input stage is proposed. In this scheme, a combination of coupled inductors in the input stage is utilized. The input stage is able to easily reject out-band interference with 29.6 dB. This input stage is applied in an LNA with 0.18 μm technology. The LNA has a peak gain of 24 dB in 3.1–10.6 GHz frequency band while showing a minimum noise figure of 1.44 dB in the mentioned frequency band. Power consumption of the UWB LNA core is 14.1 mW DC which is supplied from a 1.8 V power supply. S11 is less than −10.3 dB over the entire bandwidth since the best value of IIP3 over the entire bandwidth is −13 dBm which occurs at the frequency of 6GHz.
Deficiency of the Long Pentraxin PTX3 Promotes Vascular Inflammation and Atherosclerosis

Background— Immune responses participate in several phases of atherosclerosis; there is, in fact, increasing evidence that both adaptive immunity and innate immunity tightly regulate atherogenesis. Pentraxins are a superfamily of acute-phase proteins that includes short pentraxins such as C-reactive protein or long pentraxins such as PTX3, a molecule acting as the humoral arm of innate immunity. To address the potential role of PTX3 in atherogenesis, we first investigated the expression of PTX3 during atherogenesis, generated double-knockout mice lacking PTX3 and apolipoprotein E, and then studied the effect of murine PTX3 deficiency on plasma lipids, atherosclerosis development, and gene expression pattern in the vascular wall. Methods and Results— PTX3 expression increases in the vascular wall of apolipoprotein E–knockout mice from 3 up to 18 months of age. Double-knockout mice lacking PTX3 and apolipoprotein E were fed an atherogenic diet for 16 weeks. Aortic lesions were significantly increased in double-knockout mice and mice heterozygous for PTX3 compared with apolipoprotein E–knockout mice. Mice lacking PTX3 showed a more pronounced inflammatory profile in the vascular wall as detected by cDNA microarray and quantitative polymerase chain reaction analysis and an increased macrophage accumulation within the plaque. Finally, lesion size correlated with the number of bone marrow monocytes. Conclusion— PTX3 has atheroprotective effects in mice, which, in light of the cardioprotective effects recently reported, suggests a cardiovascular protective function of the long pentraxin 3 through the modulation of the immunoinflammatory balance in the cardiovascular system.
Systematic Analysis of Absorbed Anti-Inflammatory Constituents and Metabolites of Sarcandra glabra in Rat Plasma Using Ultra-High-Pressure Liquid Chromatography Coupled with Linear Trap Quadrupole Orbitrap Mass Spectrometry

Ultra-high-pressure liquid chromatography (UHPLC) was coupled with linear ion trap quadrupole Orbitrap mass spectrometry (LTQ-Orbitrap) and was used for the first time to systematically analyze the absorbed components and metabolites in rat plasma after oral administration of the water extract of Sarcandra glabra. This extract is a well-known Chinese herbal medicine for the treatment of inflammation and immunity related diseases. The anti-inflammatory activities of the absorbed components were evaluated by measuring nitric oxide (NO) production and proinflammatory genes expression in lipopolysaccharide (LPS)-stimulated murine RAW 264.7 macrophages. As a result, 54 components in Sarcandra glabra were detected in dosed rat plasma, and 36 of them were positively identified. Moreover, 23 metabolites were characterized and their originations were traced. Furthermore, 20 of the 24 studied components showed anti-inflammatory activities. These results provide evidence that this method efficiency detected constituents in plasma based on the anti-inflammatory mechanism of multiple components and would be a useful technique for screening multiple targets for natural medicine research.
Systematic mapping study on high-level language virtual machines

Background: There is a large body of literature on research in virtual machine for high-level languages, i.e., high-level language virtual machines (HLL VMs). Despite being a well-established research area, there are no studies focusing on characterizing the sorts of research that have been conducted and shedding light on most investigated subjects as well as subjects requiring further research. Objectives: To conduct a systematic mapping study of the literature describing research into HLL VM. Research method: We undertook a systematic mapping study of the literature based upon searching of major electronic databases. Results: 128 papers have been selected and classified by their contribution, employed HLL VM implementation, type and date of publication. Conclusions: The majority of the selected studies concentrate on improvements for boosting performance, introducing better garbage collection capabilities, and adapting HLL VMs or their core components to meet the requirements for embedded platforms. Furthermore, from examining the selected studies we have found that Java virtual machine (JVM) implementations are by far the most employed within academic settings. Among them, Jikes Research Virtual Machine is the most-widely used.
Differenciated bandwidth allocation in P2P layered streaming

There is an increasing demand for P2P streaming in particular for layered video. In this category of applications, the stream is composed of hierarchically encoded sub-streams layers namely the base layer and enhancements layers. We consider a scenario where the receiver peer uses the pull-based approach to adjust the video quality level to their capability by subscribing to different number of layers. We note that higher layers received without their corresponding lower layers are considered as useless and cannot be played, consequently the throughput of the system will drastically degrade. To avoid this situation, we propose an economical model based on auction mechanisms to optimize the allocation of sender peers' upload bandwidth. The upstream peers organize auctions to “sell” theirs items (links' bandwidth) according to bids submitted by the downstream peers taking into consideration the peers priorities and the requested layers importance. The ultimate goal is to satisfy the quality level requirement for each peer, while reducing the overall streaming cost. Through theoretical study and performance evaluation we show the effectiveness of our model in terms of users and network's utility.
Optimal loop bandwidth design for low noise PLL applications

This paper presents a salient method to find an optimal bandwidth for low noise phase-locked loop (PLL) applications by analyzing a discrete-time model of charge-pump PLLs based on ring oscillator VCOs. The analysis shows that the timing jitter of the PLL system depends on the jitter in the ring oscillator and an accumulation factor which is inversely proportional to the bandwidth of the PLL. Further analysis shows that the timing jitter of the PLL system, however, proportionally depends on the bandwidth of tile PLL when an external jitter source is applied. The analysis of the PLL timing jitter of both cases gives the clue to the optimal bandwidth design for low noise PLL applications. Simulation results using a C-language PLL model are compared with the theoretical predictions and show good agreement.
Nonintrusive Failure Detection and Recovery for Internet Services Using Backdoors ∗

We describe an architecture for nonintrusive failure detection and recovery in a cluster of Internet servers in which nodes mutually monitor their liveness and recover client sessions from failed nodes. The system is based on Backdoors, a novel architectural approach for remote healing of computer systems. Backdoors enables monitoring and recovery/repair of state in a computer system by remote access to system resources (memory, I/O devices) without using its processors. Backdoors allows remote actions to be performed with no overhead, and even when the processors (but not the memory) of a machine are not available. We have implemented a Backdoors prototype by modifying the FreeBSD kernel and using Myrinet NICs for remote access. The system uses remote DMA operations to perform monitoring, detect failures and extract OS and application state from a failed machine. We have used our system to run several open-source Internet servers and to run a complex multi-tier e-commerce application. The system tolerates multiple node failures while providing correct and continuous service to ongoing sessions, with negligible disruption.
Comparative Analysis of Universal Gates using MCML and CMOS Technique

MOS current mode logic (MCML) is an emerging logic family which is gaining attention due to its high speed of operation, robust performance and presence of mere switching noise as compared to the CMOS logic family. In this paper we have compared universal gates using MCML and conventional CMOS in terms of power and propagation delay at 16-nm Technology node. Comparative analysis shows that MCML universal gates has less power and delay as compared to conventional CMOS based universal gates at 16 nm technology. Variability analysis establishes MCML based universal gates as the most resilient and immune to various electrical parameters.
Hepatitis C viral infection increases the risk of lymphoid‐neoplasms: A population‐based cohort study

Chronic hepatitis C viral (HCV) infection has been associated with non‐Hodgkin's lymphoma (NHL); however, the results are inconsistent among regions with different HCV prevalence rates. The temporal relationship, risk estimates, and association between HCV and lymphoid‐neoplasms remain unclear. This study investigated the temporal relationship between HCV infection and lymphoid‐neoplasms using a nationwide population‐based cohort. Patients with chronic HCV infection were retrieved from the Taiwan National Health Insurance Research Database during 2001‐2005 and designated as the HCV cohort. Those with prior malignancies or coinfected with hepatitis B or human immunodeficiency virus were excluded. The age, sex, and comorbidities, including rheumatological disorders and diabetes, were matched by propensity scores to another non‐HCV cohort. Both cohorts were followed longitudinally until 2009 for a new diagnosis of any lymphoid‐neoplasms or NHL. A total of 11,679 HCV and 46,716 non‐HCV patients were included and followed for 8 years. The incidence rates of any lymphoid‐neoplasms and NHL were significantly greater in the HCV cohort than the non‐HCV cohort (48.4 versus 22.1, and 37.0 versus 17.5 per 100,000 person‐years, respectively, both P < 0.001), even after we excluded lymphoid‐neoplasms developed within the first year of follow‐up. Cox proportional hazards regression analysis (after adjustment for age, sex, numbers of annual medical visits during follow‐up, and comorbidities) indicated that HCV infection was associated with an increased risk of either any lymphoid‐neoplasms (hazard ratio = 2.30, 95% confidence interval 1.55‐3.43, P < 0.0001) or NHL (hazard ratio = 2.00, 95% confidence interval 1.27‐3.16, P = 0.003). Conclusion: After adjustment for confounders and biases, chronic HCV infection is temporally associated with a two‐fold increased risk of lymphoid‐neoplasms, especially NHL, in Asian patients; additional large studies are needed to explore whether HCV eradication can reduce the incidence of lymphoid‐neoplasms. (Hepatology 2016;63:721–730)
Intravitreal triamcinolone acetonide for exudative age related macular degeneration

Aim: To evaluate the effect of intravitreal triamcinolone acetonide on the visual acuity of patients with exudative age related macular degeneration, to assess the duration of a possible effect, and to evaluate clinical side effects of the treatment. Methods: The study included 67 patients (71 eyes) who presented with exudative age related macular degeneration of predominantly or total occult type (n = 68) or classic type (n = 3), and who received once, or repeatedly, an intravitreal injection of 25 mg of crystalline triamcinolone acetonide. Mean follow up time was 7.46 (SD 3.54) months (range 3.1–19.57 months). Results: Visual acuity increased significantly (p <0.001) from 0.16 (0.11) to a mean maximum of 0.23 (0.17). Postoperative visual acuity was highest 1–3 months after the injection. 47 (66.2%) eyes gained in maximal visual acuity and 11 (15.5%) eyes lost in visual acuity. Intraocular pressure increased significantly (p <0.001) from 15.1 (3.1) mm Hg at baseline to a maximal value of 23.0 (8.25) mm Hg. At the end of follow up, intraocular pressure again decreased significantly (p<0.001) to 16.8 (4.9) mm Hg. No cases of postoperative infectious endophthalmitis, rhegmatogenous retinal detachment, or proliferative vitreoretinopathy occurred. Owing to a decrease in visual acuity after an initial increase, six patients received a second intravitreal triamcinolone acetonide injection after which visual acuity increased again in three eyes. Conclusions: Intravitreal injection of 25 mg of crystalline triamcinolone acetonide merits further study for the treatment of exudative age related macular degeneration.
Smooth Pulse Generation by a Q-Switched Erbium-Doped Fiber Laser

A Q-switched Erbium-doped fiber laser with symmetric cavity design is thoroughly investigated. It is shown theoretically and verified experimentally that such a laser is capable of generating stable giant pulses with smooth temporal shape and maximized peak power ( ~ 40 W) and minimized duration ( ~ 30 ns), as compared with an analogous laser having conventional asymmetric cavity. The principle that stands behind this performance is also discussed.
RAID-II: Design and implementation of a large scale disk array controller

We describe the implementation of a large scale disk array controller and subsystem incorporating over 100 high performance 3.5 inch disk drives. It is designed to provide 40 MB/s sustained performance and 40 GB capacity in three 19 inch racks. The array controller forms an integral part of a file server that attaches to a Gb/s local area network. The controller implements a high bandwidth interconnect between an interleaved memory, an XOR calculation engine, the network interface (HIPPI), and the disk interfaces (SCSI). The system is now functionally operational, and we are tuning its performance. We review the design decisions, history, and lessons learned from this three year university implementation effort to construct a truly large scale system assembly.
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.
Coccolith Sr/Ca as a new indicator of coccolithophorid calcification and growth rate

Polyspecific coccolith separates from core top sediments in the eastern equatorial Pacific show variations of ∼15% in Sr/Ca ratios across the equatorial upwelling zone, with Sr/Ca highest at the equator and decreasing off‐axis. These variations cannot be due to changes in the Sr/Ca of seawater, which varies by less than 2% in the surface ocean. Variations in Sr/Ca of coccolith sediments are similar to variations in primary productivity and alkenone‐estimated coccolithophorid growth rates in overlying surface waters and to CaCO3 rain rates measured in sediment traps. Because of these relationships and because calcification rate exerts a strong control on Sr/Ca in abiogenic calcites, we suggest that the observed Sr/Ca variations in coccoliths may be strongly controlled by coccolithophorid growth and calcification rates, although temperature may also influence coccolith Sr/Ca to a lesser degree. Changes in dissolution intensity and coccolith assemblages appear to exert a minor influence, if any, on coccolith Sr/Ca in these sediment core tops. If further work confirms relationships between coccolith Sr/Ca and coccolithophorid productivity, Sr/Ca records of past changes in coccolithophorid productivity may be useful in reconstructing past variations in the rain ratio of organic to carbonate carbon, an important control on deep ocean pH and partitioning of CO2 between the atmosphere and ocean. In addition, coccolith Sr/Ca might provide an independent record of past changes in coccolithophorid growth rates, which in combination with data on the carbon isotopic fractionation in coccolithophorid organic matter may permit more reliable calculations of past dissolved CO2 in the surface ocean.