gebhart/patrepeval huggingface dataset:
Arbitrary polarization and orbital angular momentum generation based on spontaneously broken degeneracy in helically twisted ring-core photonic crystal fibers (2021)

Using orbital angular momentum (OAM) as a spatial information channel attracts a lot of attention due to its infinite multiplexing capability. The research on OAM carrying fibers is intensively studied and ring-core fibers are promising candidates for them. At the same time, generating OAM modes in those fibers are also important topic. Here, the evolutions of polarization states including OAM of light in helically twisted ring-core photonic crystal fibers (PCFs) are investigated for generating OAM states. The degeneracy of some of the mode sets is spontaneously broken, and the birefringence cause a geometric phase (GP) in the twisted PCFs while preserving the vectorial nature of the modes. It is demonstrated that an arbitrary polarization and OAM state can be generated by using the GP in uniformly twisted and twisted PCFs with periodical inversion. In the ring-core PCF presented in this paper, the degeneracy of HE<sub>31</sub> and EH<sub>31</sub> mode sets are broken, and OAM light with the topological charge of 2 and 4 can be generated. The wavelength dependence is very small compared with that of OAM generators based on long-period gratings (LPGs). Furthermore, by properly setting the period of the inversion, OAM light with different topological charges can be simultaneously generated with the same fiber structure. These results indicate that the proposed approach is effective for the generation of OAM modes with the conventional fiber modes.
Circulating biomarkers to monitor cancer progression and treatment (2016)

Tumor heterogeneity is a major challenge and the root cause of resistance to treatment. Still, the standard diagnostic approach relies on the analysis of a single tumor sample from a local or metastatic site that is obtained at a given time point. Due to intratumoral heterogeneity and selection of subpopulations in diverse lesions this will provide only a limited characterization of the makeup of the disease. On the other hand, recent developments of nucleic acid sequence analysis allows to use minimally invasive serial blood samples to assess the mutational status and altered gene expression patterns for real time monitoring in individual patients. Here, we focus on cell-free circulating tumor-specific mutant DNA and RNA (including mRNA and non-coding RNA), as well as current limitations and challenges associated with circulating nucleic acids biomarkers.
Signal modification for voiced wideband speech coding and its application for IS-95 system (2003)

In CELP coding, signal modification is often employed to improve the pitch prediction at lowest bit rates. In this paper, a signal modification method for coding purely voiced wideband speech frames is introduced. The modification is performed frame and pitch synchronously preserving the original time scale at the end of each frame, which makes the method particularly convenient for variable bit rate coding. Special attention is paid to modify only the frames which are most suitable for the signal modification and low bit rate coding. The signal modification method is applied to a variable bit rate ACELP coder that satisfies IS-95/CDMA2000 rate-set II system requirements.
A Novel Modified Secant Method for Computing the Fair Share Rate (2005)

In this paper, we propose a novel modified secant algorithm to compute the flow fair share rate within the framework of the core-stateless fair queueing [1]. The geometric explanation and numerical results demonstrate that the proposed algorithm possesses better performance in terms of accuracy and convergence than that proposed in [1].
Myeloma light chains induce epithelial-mesenchymal transition in human renal proximal tubule epithelial cells (2007)

To determine the role of epithelial-mesenchymal transition (EMT) as a potential mechanism contributing to the characteristic tubulointerstitial renal fibrosis in multiple myeloma, we examined whether myeloma light chains (LCs) directly induce EMT in human renal proximal tubule epithelial cells (PTECs).As positive controls we used TGF-beta1 and cyclosporine A (CsA), two agents known to induce EMT in PTECs. Human LCs were isolated and purified from the urine of myeloma patients with modest renal insufficiency without evidence of glomerular involvement. HK-2 cells were exposed to kappa LC (25 microM) for periods up to 72 h.LCs induced marked cellular morphological alterations in PTECs, accompanied with increased expression levels of profibrotic TGF-beta1, FSP-1 and extracellular matrix components. Using semiquantitative immunoblotting and RT-PCR, we observed that the expression of E-cadherin decreased after 24 h, while the expression of alpha-SMA increased in PTEC after continuous exposure to kappa-LCs. Human serum albumin (HSA; 160 microM) had less potent effect on the expression of EMT-related molecules. Neutralizing TGF-beta1 antibody blocked CsA-induced EMT but had no effect on LC-exposed cells. LC-induced EMT and the secretions of IL-6 and MCP-1 were, however, markedly attenuated by p38 MAPK interference. The use of bone morphogenetic protein-7 or pituitary adenylate cyclase-activating polypeptide (PACAP) induced the formation of cell aggregates, and the reacquisition of E-cadherin expression and renal proximal tubule epithelial morphology within the confluent cell monolayer during and after LC exposure.These findings demonstrate that LC is a direct stimulus for EMT in PTECs. LC-induced EMT involved multiple cytokines, is modulated by p38 MAPK, but appeared independent of the action of TGF-beta1. LC-induced EMT may be an important mechanism of kidney injury associated with myeloma and may be reversible upon the administration of exogenous PACAP.
Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo (2017)

When a ribonucleic acid (RNA) molecule folds, it often does not adopt a single, well-defined conformation. The folding energy landscape of an RNA is highly dependent on its nucleotide sequence and molecular environment. Cellular molecules sometimes alter the energy landscape, thereby changing the ensemble of likely low-energy conformations. The effects of these energy landscape changes on the conformational ensemble are particularly challenging to visualize for large RNAs. We have created a robust approach for visualizing the conformational ensemble of RNAs that is well suited for in vitro versus in vivo comparisons. Our method creates a stable map of conformational space for a given RNA sequence. We first identify single point mutations in the RNA that maximally sample suboptimal conformational space based on the ensemble's partition function. Then, we cluster these diverse ensembles to identify the most diverse partition functions for Boltzmann stochastic sampling. By using, to our knowledge, a novel nestedness distance metric, we iteratively add mutant suboptimal ensembles to converge on a stable 2D map of conformational space. We then compute the selective 2' hydroxyl acylation by primer extension (SHAPE)-directed ensemble for the RNA folding under different conditions, and we project these ensembles on the map to visualize. To validate our approach, we established a conformational map of the Vibrio vulnificus add adenine riboswitch that reveals five classes of structures. In the presence of adenine, projection of the SHAPE-directed sampling correctly identified the on-conformation; without the ligand, only off-conformations were visualized. We also collected the whole-transcript in vitro and in vivo SHAPE-MaP for human β-actin messenger RNA that revealed similar global folds in both conditions. Nonetheless, a comparison of in vitro and in vivo data revealed that specific regions exhibited significantly different SHAPE-MaP profiles indicative of structural rearrangements, including rearrangement consistent with binding of the zipcode protein in a region distal to the stop codon.
Endoscopic Ultrasound (EUS), Chronic Pancreatitis, and Pancreatic Cancer (PC) Precursors in High Risk Individuals (2006)

EUS and ERCP in high risk individuals (HRI) with an inherited predisposition for PC have shown chronic pancreatitis (CP)-like abnormalities but the significance of these changes has not been understood. AIM: To determine the prevalence of pancreatic EUS abnormalities in asymptomatic HRI and correlate these with ERCP, pancreatic function, and pathology. Methods: In 2 prospective cohort studies (1998–2004), 112 HRI (105 HRI with ≥2 affected first degree relatives with PC, 7 had Peutz-Jeghers syndrome) had screening EUS. ERCP was performed by another endoscopist without knowledge of EUS findings. Serum trypsin and secretin stimulated-peak bicarbonate concentration was measured in HRI and normal controls. Surgery was performed for suspected neoplasms or dysplastic tissue in EUS-FNA. Pancreata were examined by an experienced pathologist. Results: The prevalence of EUS changes of CP (≥4 of 9 features) in HRI was 72.3%. Mild ERCP abnormalities were present in 85.6%. Serum trypsin was lower in HRI than in controls (mean=66.4 vs. 169.1, p=.0001). But, mean peak bicarbonate concentration was similar in HRI and controls (106.8 meq/L vs. 105.4 meq/L, respectively, p=0.83). Subtotal pancreatectomy was performed on 15 HRI: pancreatic neoplasms were found in 11 and pancreatic intraepithelial neoplasia (PanIN) 1–3 were present in 13. The mean PanIN density in HRI pancreata was 12.2% (range 1–27.3%). Both IPMNs and PanIN were associated with parenchymal lobulocentric atrophy and CP. PanIN density was positively and linearly correlated with the number of EUS features of CP (Spearman's R=0.87, p=.005) but not ERCP grade of CP (Spearman's R=0.41, p=.31). Conclusions: EUS features of CP are highly prevalent in HRI with an inherited predisposition to PC and are associated with both IPMN and PanI. EUS features of CP correlate with PanIN density and PanIN-associated lobulocentric atrophy.
Winged bean [Psophorcarpus tetragonolobus (L.) DC] seeds as an underutilised plant source of bifunctional proteolysate and biopeptides (2014)

Hypertension is one of the major causes of cardiovascular-related diseases, which is highly associated with angiotensin-I-converting enzyme (ACE) activity and oxidative stress. In this study, winged bean seed (WBS), a potential source of protein, was utilised for the production of bifunctional proteolysate and biopeptides with ACE inhibitory and antioxidative properties. An enzymatic approach was applied, coupled with pretreatment of shaking and centrifuging techniques to remove endogenous ACE inhibitors prior to proteolysis. ACE inhibition reached its highest activity, 78.5%, after 12 h proteolysis while antioxidative activities, determined using assays involving DPPH˙ radical scavenging activity and metal ion-chelating activity, reached peaks of 65.0% and 65.7% at 8 h and 14 h, respectively. The said bioactivities were proposed to share some common structural requirements among peptides. A two-dimensional approach was employed for characterisation of effective peptides based on hydrophobicity, using RP-HPLC, and isoelectric property, using isoelectric focusing technique. Results revealed that acidic and basic peptides with partially higher hydrophobicity provided higher ACE inhibition activity than did neutral peptides. Finally, by using Q-TOF mass spectrometry, two peptide sequences (YPNQKV and FDIRA) with ACE inhibitory and antioxidative activities were successfully matched with a database. This study indicates that the WBS proteolysate can be a potential bifunctional food ingredient as the identified biopeptides demonstrated both ACE inhibitory and antioxidative activities in vitro.
[Development of the detection system for Mycobacterium tuberculosis DNA by using the isothermal DNA amplification method ICAN]. (2002)

The isothermal and chimeric primer-initiated amplification of nucleic acids(ICAN) is a new isothermal DNA amplification method composed of exo- Bca DNA polymerase, RNaseH and DNA-RNA chimeric primers. We developed the detection system, combined the ICAN with luminescence detection by a probe hybridization, for Mycobacterium tuberculosis DNA targeting the IS6110 insertion element. We examined performance tests of the system. This system was able to detect one copy of Mycobacterium tuberculosis DNA for only 3.5 hours, and performance of the system was equivalent or better to the Roche PCR system. We also examined a detection system by using magnetic beads, which system could shorten detection time for 2.5 hours. It was shown that the ICAN system was an efficient and sensitive detection system for Mycobacterium tuberculosis DNA from mass samples.
Skeletal Mechanism for NOx Chemistry in Diesel Engines (1998)

&lt;div class="htmlview paragraph"&gt;Most computational schemes and kinetic models for engine-out NO&lt;sub&gt;x&lt;/sub&gt; emissions from Diesels are based on the Zeldovich or extended Zeldovich mechanism. However, at pressures typical of both the premixed and diffusion portions of the combustion process, the third-body reaction leading to the formation of N&lt;sub&gt;2&lt;/sub&gt;O (O + N&lt;sub&gt;2&lt;/sub&gt; + M) becomes faster than the leading reaction in the Zeldovich mechanism (O + N&lt;sub&gt;2&lt;/sub&gt;). As in gas turbines, particularly those involving lean-premixed combustor designs, NO formation in Diesels through the N&lt;sub&gt;2&lt;/sub&gt;O mechanism can thus proceed more efficiently than through the traditional route. Decomposition of NO in the combustion products during the power stroke can also occur by both the reverse Zeldovich reactions and the second order step that produces N&lt;sub&gt;2&lt;/sub&gt;O (2NO ® N&lt;sub&gt;2&lt;/sub&gt;O + O).&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Based on these observations, a skeletal mechanism consisting of seven elementary reactions is used to develop a two-zone model for NO&lt;sub&gt;x&lt;/sub&gt; emissions from direct injection (DI) Diesel engines. To evaluate the chemistry in the first zone where NO forms, the stoichiometric flame temperature and corresponding equilibrium burned gas conditions are computed at start of combustion conditions. The second zone is that in which the NO formed in zone 1 decomposes and is characterized with the equilibrium composition and flame temperature at the end of combustion, based on a fuel/air dual cycle analysis.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Characteristic chemical times for NO formation in zone 1 and NO decomposition in zone 2 are formulated from the law of mass action applied separately to each zone. The ratio of the value for decomposition to that for formation is easily computed from equilibrium analyses at the stoichiometric and overall equivalence ratios. The utility of using this ratio to evaluate the influence of decomposition upon exhaust emissions is examined. A general chart is presented, in which the logarithm of this kinetic time ratio is graphed versus reciprocal end-of-combustion flame temperature. Lines of constant pressure at start of combustion (representing turbocharger boost ratio, engine compression ratio, and injection timing) and constant peak engine pressure allow approximate positioning for any engine on the chart as a function of load once preliminary design is completed. In general, the chart suggests that decomposition of NO becomes increasingly significant as engine load (end-of-combustion flame temperature) is increased. Finally, the kinetic time ratios are computed for operating conditions typical of one light-duty and three heavy-duty turbocharged engines and found entirely consistent with results deduced from the general chart.&lt;/div&gt;
Performance Testing and Analysis of Synchronous Reluctance Motor Utilizing Dual-Phase Magnetic Material (2018)

While interior permanent magnet (IPM) machines have been considered state of the art for traction motors, synchronous reluctance (SynRel) motors with advanced materials can provide a competitive alternative. IPM machines typically utilize neodymium iron boron permanent magnets, which pose an issue in terms of price, sustainability, demagnetization at higher operating temperatures, and uncontrolled generation. On the other hand, SynRel machines do not contain any magnets and are free from these issues. However, the absence of magnets as well as the presence of bridges and centerposts limit the flux-weakening capability of a SynRel machine, and limit the achievable constant power speed ratio without having to significantly oversize the machine and/or the power converter. In this paper, a new material referred to as the dual-phase magnetic material, where nonmagnetic regions can be selectively introduced within each lamination, will be evaluated for SynRel designs. The dual-phase feature of this material enables nonmagnetic bridges and posts, eliminating one of the key limitations of the SynRel designs in terms of torque density and flux weakening. This paper will present the design, analysis, and test results of an advanced proof-of-concept SynRel design utilizing dual-phase material with traction applications as the ultimate target application.
THz in biology and medicine: toward quantifying and understanding the interaction of millimeter- and submillimeter-waves with cells and cell processes (2010)

As the application and commercial use of millimeter- and submillimeter-wavelength radiation become more widespread, there is a growing need to understand and quantify both the coupling mechanisms and the impact of this long wavelength energy on biological function. Independent of the health impact of high doses of radio frequency (RF) energy on full organisms, which has been extensively investigated, there exists the potential for more subtle effects, which can best be quantified in studies which examine real-time changes in cellular functions as RF energy is applied. In this paper we present the first real time examination of RF induced changes in cellular activity at absorbed power levels well below the existing safe exposure limits. Fluorescence microscopy imaging of immortalized epithelial and neuronal cells in vitro indicate increased cellular membrane permeability and nanoporation after short term exposure to modest levels (10-50 mW/cm<sup>2</sup>) of RF power at 60 GHz. Sensitive patch clamp measurements on pyramidal neurons in cortical slices of neonatal rats showed a dramatic increase in cellular membrane permeability resulting either in suppression or facilitation of neuronal activity during exposure to sub-&mu;W/cm<sup>2</sup> of RF power at 60 GHz. Non-invasive modulation of neuronal activity could prove useful in a variety of health applications from suppression of peripheral neuropathic pain to treatment of central neurological disorders.
Forging reform in China the fate of state-owned industry (1998)

The greatest economic challenge facing China in the post-Deng era is the reform of unprofitable, state-owned enterprises (SOEs) which threaten to drag down the rest of the economy. Despite an array of well-intentioned, market-oriented reform measures, these firms have never truly been forced to face the pressure of a bottom line, or the threat of bankruptcy. Forging Reform in China explains how and why these measures have not been sweepingly successful to date, and what it would take to achieve meaningful reform. The author investigates firm-level processes, including case studies of China's steel industry giants, revealing institutional and systemic barriers to market-oriented performance. This book makes a compelling argument that private ownership cannot work in China's current system until governance over complex economic factors has been established, that is, until credit is tightened and market selection processes made to work
Investigation of coherent receiver designs in high-speed optical inter-satellite links using digital signal processing (2017)

Due to higher data rates, better data security and unlicensed spectral usage optical inter-satellite links (OISL) offer an attractive alternative to conventional RF-communication. However, the very high transmission distances necessitate an optical receiver design enabling high receiver sensitivity which requires careful carrier synchronization and a quasi-coherent detection scheme.
On the performance limits of data-aided synchronization (2003)

This paper addresses data-aided (DA) synchronization, in which the reference parameter acquisition is aided by a training sequence known to the receiver. The Cramer-Rao lower bound (CRB) for the DA timing and/or carrier phase recovery is presented. For DA parameter estimation, the CRB typically varies with the training sequence. This indicates that different training sequences offer fundamentally different performance. In the literature, the widely cited closed-form CRB for timing and carrier phase recovery was derived under the assumption that the training sequence is independent and identically distributed (i.i.d.) and sufficiently long. We derive a closed-form CRB for timing and carrier phase recovery with respect to an arbitrary training sequence and pulse shaping function for the over and under sampling cases. It turns out that the CRB is a weighted summation of the aperiodic correlation of the training sequence and the weighting factor is determined by the pulse shaping filter. Therefore, this paper reveals the fundamental link between a training sequence and its corresponding performance limit.
Experimental comparison of WDM system capacity in conventional and nonzero dispersion shifted fiber (1999)

A primary consideration in designing new backbone optical network segments is the total data capacity of each fiber span. We compare the wavelength-division-multiplexed capacity of conventional single-mode fiber (SMF) and nonzero dispersion shifted fiber by measuring performance versus channel spacing in 4/spl times/80 km transmission of five 10 Gb/s channels at the nominal commercial erbium-doped fiber amplifier power specification of 9 dBm/ch. The achievable capacity is found to be more than four times greater in conventional SMF.
Phagocytic Activity and Monocyte Chemotactic Protein Expression by Pulmonary Macrophages in Persistent Pulmonary Cryptococcosis (2003)

The mechanisms by which Cryptococcus neoformans persists in an immunocompetent host are not well understood. Using a rat model of persistent infection, we investigated the ability of pulmonary macrophages (PuM) to phagocytize C. neoformans and produce monocyte chemotactic protein 1 (MCP-1) as a function of the length of time of infection and opsonin. The ability of macrophages to affect serum-mediated phagocytosis varied over the course of infection and was dependent on CD11b/c and CD18 expression. Infection resulted in increased MCP-1 levels within the lung, though the actual amounts varied over the course of infection. Immunohistochemical studies localized MCP-1 expression to macrophages and epithelioid cells. Enhanced production of MCP-1 by PuM from infected rats was confirmed by ex vivo studies. Induction of MCP-1 following serum-mediated phagocytosis was observed for PuM from both infected and noninfected rats and depended on the interaction of C. neoformans with CD11b/c and CD18. Specific antibody was more efficient than serum in promoting phagocytosis and consistently elicited more MCP-1. The relative amount of MCP-1 produced in association with phagocytosis was similar for PuM at all lengths of time of infection. Decreased MCP-1 production was observed for PuM obtained from older rats, including long-term (8 to 10 months)-infected and age-matched controls, suggesting that aging may affect the production of MCP-1 by PuM in response to cryptococcal infection. In summary, our results show that macrophages are an important source of MCP-1 during pulmonary cryptococcosis and that MCP-1 production is actively regulated during infection. Furthermore, we find that phagocytosis of C. neoformans can serve as an important stimulus for MCP-1 production by PuM, though the efficiency of this process is dependent on the opsonin type and may be affected by aging.