Miracle-dz/UniFAR-FTUs huggingface dataset:
A discrete model for Networked Labs-on-Chips: Linking the physical world to design automation

Labs-on-Chip integrate and minimize the functionality of complete conventional laboratories on a single chip. An upcoming and especially biocompatible realization are Networked Labs-on-Chips (NLoCs). In NLoCs, small volumes of reagents, so-called droplets, flow in an immiscible fluid in closed channels. An external pump applies a force to this immiscible fluid driving the droplets through the channels of the NLoC. However, the exact flow behavior of droplets in NLoCs physically depends on many factors and interdependencies. This makes it cumbersome to manually determine the taken path of a droplet and the time it needs to pass the NLoC. For the same reason, also almost no automated design solutions exist for NLoCs yet. In this work, we present a discrete model enabling designers and design automation tools to efficiently determine the droplets' path and positions. The precision of the proposed model is evaluated by a systematic examination for basic building blocks of NLoCs as well as for a complete architecture. The resulting model can be used for manual inspections of the droplets' behavior in an NLoC and, additionally, provides the basis for automated design solutions.
Modeling Quantum Transport in Nanoscale Transistors

Venugopal, Ramesh. Ph.D., Purdue University, August, 2003. Modeling Quantum Transport in Nanoscale Transistors. Major Professor: Mark Lundstrom. As critical transistor dimensions scale below the 100 nm (nanoscale) regime, quantum mechanical effects begin to manifest themselves and affect important device performance metrics. Therefore, simulation tools which can be applied to design nanoscale transistors in the future, require new theory and modeling techniques that capture the physics of quantum transport accurately and efficiently. This thesis outlines a rigorous yet practical approach to model quantum transport in nanoscale silicon transistors based on the non-equilibrium Green’s function (NEGF) formalism. The objectives of this thesis are: 1) to implement the appropriate physics and methodology for nanoscale device modeling 2) to develop new TCAD (technology computer aided design) tools for quantum scale device simulation and 3) to examine and assess new features of carrier transport in futuristic nanoscale transistors. Technical issues are investigated by simulating transistors with a silicon-on-insulator (SOI) device geometry, which is widely accepted as the ideal device structure for scaling silicon technology to its fundamental limits. Simulation results presented in this thesis are used to highlight important aspects of carrier transport such as quantum coherence, confinement and tunneling, self-consistent band lineup, the nature of the voltage drop, the role of scattering and the behavior of the current versus voltage characteristics for transistors with differing geometries.
Primary Medullary Hemorrhage: Report of Four Cases and Review of the Literature

Background Primary medullary hemorrhage is uncommon. Its clinical profile and prognosis are not well known. We report four cases of medullary hemorrhage and a review of the English and French literature since 1964 to analyze the clinical presentation and prognosis. Case Descriptions Of sixteen case reports of medullary hemorrhage reviewed from the literature, sixteen contained sufficient information for review and are included in this report. The age distribution of the patients was between 13 and 72 years, and 10 of these patients were men. The most frequent symptoms at onset were vertigo, sensory symptoms, and dysphagia. Presenting signs included palatal weakness, nystagmus, hypoglossal palsy, cerebellar ataxia, and limb weakness. The diagnosis was made at autopsy in 3 patients, at surgery in 3, by computed tomography in 4, and more recently by magnetic resonance imaging in 6. In nine instances the etiology of hemorrhage was undetermined; a ruptured vascular malformation was the cause in 3 patients, 1 was attributed to the use of anticoagulants, and hypertension was the suspected cause in the other 3 patients. Mortality rate was 19%; however, survivors generally had nonincapacitating sequelaes. Conclusions These findings indicate that primary medullary hemorrhage presents with a characteristic syndrome of sudden onset of headache and vertigo with neurological signs that correspond to various combinations of medial and lateral medullary involvement. In those patients who survive, prognosis usually is good.
Administration of the p38 MAPK inhibitor SB203580 affords brain protection with a wide therapeutic window against focal ischemic insult

We have reported previously the delayed and differential induction of p38α and p38β mitogen‐activated protein kinases (MAPKs) in microglia and astrocytes, respectively, in brain after transient global ischemia. We report here the sustained induction and activation of p38α MAPK in activating microglia in rat brain after transient middle cerebral artery occlusion (MCAO). The intraventricular administration of SB203580, a p38 MAPK inhibitor, 30 min before MCAO reduced the infarct volume to 50% of the control, which was accompanied by the significant improvement of neurological deficits. More interestingly, the infarct volume was reduced to 72% and 77% when SB203580 was administered 6 hr and 12 hr after MCAO, respectively. The induction of various factors involved in inflammatory processes, such as inducible nitric oxide synthase (iNOS), tumor necrosis factor‐α (TNF‐α), interleukin‐1β (IL‐1β) and cyclooxygenase‐2 (COX‐2), was suppressed by the administration of SB203580 at 6 hr after MCAO. These results suggest that sustained activation of p38 MAPK pathway and p38 MAPK‐associated inflammatory processes play a crucial role in postischemic brain. © 2003 Wiley‐Liss, Inc.
Human Papillomavirus Testing in Primary Cervical Screening and Abnormal Papanicolaou Management

Human papillomavirus (HPV) infection is a necessary cause of cervical cancer; HPV testing capitalizes on this fact to maximize the clinical benefits of cervical screening and abnormal Papanicolaou (Pap) test management. HPV tests in combination with Pap tests are 96% to 100% sensitive for detection of cervical intraepithelial neoplasia (CIN) 2/3 and cancer. However, because HPV infection is common in young women and most commonly transient, HPV testing is not recommended as part of primary cervical screening for women younger than 30 years of age. HPV testing is recommended for women of any age for the clarification of atypical cells of undetermined significance (ASC-US) results and as an option for follow up of women with HPV-positive ASC-US, atypical squamous cells “cannot rule out high-grade,” or low-grade squamous intraepithelial lesions not found to have CIN 2/3. HPV testing is also recommended as an alternative to colposcopy and/or cytology for follow up of treated cases. Proper use of HPV testing improves the management of women with cytologic abnormalities. In addition, a negative HPV test in combination with a normal Pap test result in women age 30 and older allows the safe extension of the interval between cervical screenings. Thus, when used properly, HPV testing may reduce morbidity and mortality and do so in a cost-effective manner.
Ammonium Concentration of Spent Medium Provides a Noninvasive Assessment of Embryonic Developmental Potential in IVF

Background: Currently, morphological criteria are used to select embryos for transfer in in vitro fertilization (IVF)-embryo transfer. However, the implantation rate is only about 30%, indicating a need for a more efficient method of selecting high-quality embryos. This study investigated the relationship between medium ammonium concentration and IVF implantation rates and evaluated the possibility of using ammonium concentration to provide an objective, noninvasive, and simple means of assessment of embryo viability. Methods: On day 3 after fertilization, we sampled the spent medium bathing embryos obtained from patients undergoing IVF or intracytoplasmic sperm injection (ICSI) at the Reproductive Medical Center of Sun Yat-sen Memorial Hospital, between September 2010 and January 2012. The concentration of ammonium was determined using a dry chemistry system. Results: The ammonium concentration increased significantly during the period of culture of all embryos, but the increase was significantly greater in the group that, subsequently, did not achieve pregnancy (P < .001). An receiver–operating characteristic (ROC) curve indicated that ammonium concentration was highly predictive of embryo implantation failure (area under ROC curve = 0.838). Failure to achieve implantation had a predictive sensitivity of 71% and specificity of 79.6%. The accuracy of prediction of successful or failed implantation was 75.4%. In both IVF and ICSI, the embryo implantation rate decreased significantly as the medium ammonium concentration increased (P < .05). Conclusion: Measurement of the ammonium concentration in the spent medium may provide a new research direction for exploring a simple, rapid, and low-cost method for reliable prediction of embryo implantation with high sensitivity and specificity.
Calcium Binding to PICK1 Is Essential for the Intracellular Retention of AMPA Receptors Underlying Long-Term Depression

NMDA receptor (NMDAR)-dependent long-term depression (LTD) in the hippocampus is mediated primarily by the calcium-dependent removal of AMPA receptors (AMPARs) from the postsynaptic density. The AMPAR-binding, PDZ (PSD-95/Dlg/ZO1) and BAR (Bin/amphiphysin/Rvs) domain-containing protein PICK1 has been implicated in the regulation of AMPAR trafficking underlying several forms of synaptic plasticity. Using a strategy involving small hairpin RNA-mediated knockdown of PICK1 and its replacement with recombinant PICK1, we performed a detailed structure–function analysis of the role of PICK1 in hippocampal synaptic plasticity and the underlying NMDAR-induced AMPAR trafficking. We found that PICK1 is not necessary for maintenance of the basal synaptic complement of AMPARs or expression of either metabotropic glutamate receptor-dependent LTD or NMDAR-dependent LTP. Rather, PICK1 function is specific to NMDAR-dependent LTD and the underlying AMPAR trafficking. Furthermore, although PICK1 does not regulate the initial phase of NMDAR-induced AMPAR endocytosis, it is required for intracellular retention of internalized AMPARs. Detailed biophysical analysis of an N-terminal acidic motif indicated that it is involved in intramolecular electrostatic interactions that are disrupted by calcium. Mutations that interfered with the calcium-induced structural changes in PICK1 precluded LTD and the underlying NMDAR-induced intracellular retention of AMPARs. These findings support a model whereby calcium-induced modification of PICK1 structure is critical for its function in the retention of internalized AMPARs that underlies the expression of hippocampal NMDAR-dependent LTD.
Decentralized multi-agent control from local LTL specifications

We propose a methodology for decentralized multi-agent control from Linear Temporal Logic (LTL) specifications. Each agent receives an independent specification to formally synthesize its own hybrid controller. Mutual satisfiability is not a priori guaranteed. Due to limited communication, the agents utilize meeting events to exchange their controller automata and verify satisfiability through model checking. Local interaction only when common atomic propositions exist reduces the overall computational cost, facilitating scalability. Provably correct collision avoidance and convergence is ensured by Decentralized Multi-Agent Navigation Functions.
Angiotensin II type I receptor (AT1R) is an independent prognosticator of esophageal squamous cell carcinoma and promotes cells proliferation via mTOR activation

Background The aim of this study was to investigate the effects of the angiotensin II/ angiotensin II type I receptor (AT1R) and angiotensin II type II receptor (AT2R) signaling pathway in esophageal squamous cell carcinoma (ESCC). Methods Immunohistochemistry was performed to evaluate the expression levels of AT1R and AT2R in tissues from 152 surgically resected ESCC patients, and those expression levels were then correlated with treatment outcomes. The angiotensin II/AT1R/AT2R signaling pathway and its biological effects in the context of ESCC were investigated in vitro and in vivo. Results In human samples, AT1R overexpression was univariately associated with inferior overall survival and remained multivariately independent (hazard ratio=1.812). In vitro, angiotensin II stimulated the growth of ESCC cells in a dose-dependent manner. Treatment with irbesartan or AT1R-RNAi knockdown but not treatment with PD123319 significantly decreased the level of angiotensin II-induced ESCC cell proliferation. Angiotensin II also caused mTOR activation in a dose-dependent manner, and everolimus or mTOR-RNAi knockdown significantly suppressed the level of angiotensin II-induced ESCC cell proliferation. Furthermore, AT1R-RNAi knockdown suppressed the activation of mTOR. Clinically, AT1R expression was also correlated with phosphorylated mTOR expression. In a xenograft model, local angiotensin II injection enhanced tumor growth, and this effect could be decreased by treatment with irbesartan or everolimus. In a 4-NQO-induced-ESCC murine model, irbesartan significantly decreased the incidence of esophageal tumor. Conclusions These findings suggest that AT1R overexpression is an independent adverse prognosticator for patients with ESCC and that angiotensin II/AT1R signaling stimulates ESCC growth, in part through mTOR activation.
Overexpression of Decorin by Rat Arterial Smooth Muscle Cells Enhances Contraction of Type I Collagen In Vitro

Objective—Overexpression of decorin reduces neointimal thickening in balloon-injured carotid arteries of rats by decreasing the volume of neointimal extracellular matrix (ECM). We examined the hypothesis that decorin regulates ECM volume by stimulating cell-mediated contraction of collagen-rich ECMs. Methods and Results—Rat arterial smooth muscle cells (ASMCs) transduced with bovine decorin cDNA by retroviral transfection (LDSN) exhibited enhanced contraction of collagen gels in vitro when compared with vector-only transduced (LXSN) cells. Addition of recombinant decorin to LXSN or LDSN cells did not stimulate contraction of collagen gels. Enhanced contraction of collagen by LDSN cells was unaffected by the metalloproteinase inhibitor GM6001. LDSN cells exhibited increased expression of type I collagen mRNA when compared with that of LXSN cells. Correspondingly, collagen gel contraction by LDSN cells was reduced by inhibition of collagen synthesis by 3,4-l-dehydroproline (L-DHP). Antibodies to &agr;1&bgr;1-integrin, but not to &agr;2&bgr;1-integrin, blocked collagen contraction by both LXSN and LDSN cells. However, LXSN and LDSN cells expressed similar levels of &agr;1- and &bgr;1-integrin mRNAs. Conclusions—Decorin synthesized de novo by ASMCs increases type I collagen synthesis and enhances contraction of collagen gels. Regulated synthesis of decorin may be a useful therapeutic approach to reduce ECM volume in vascular disease.
Cigarette smoking and the incidence of breast cancer.

BACKGROUND Tobacco smoke contains carcinogens, which may increase the risk of breast cancer (BC). Conversely, cigarette smoking also has antiestrogenic effects, which may reduce the risk of BC. The association between smoking and BC remains controversial. METHODS Prospective cohort study of 111 140 participants of the Nurses' Health Study from 1976 to 2006 for active smoking and 36 017 women from 1982 to 2006 for passive smoking. RESULTS During 3 005 863 person-years of follow-up, 8772 incident cases of invasive BC were reported. After adjustment for potential confounders, the hazard ratio (HR) of BC was 1.06% (95% confidence interval [CI], 1.01%-1.10%) for ever smokers relative to never smokers. Breast cancer incidence was associated with a higher quantity of current (P for trend = .02) and past (P for trend = .003) smoking, younger age at smoking initiation (P for trend = .01), longer duration of smoking (P for trend = .01), and more pack-years of smoking (P for trend = .005). Premenopausal smoking was associated with a slightly higher incidence of BC (HR, 1.11; 95% CI, 1.07-1.15 for every increase of 20 pack-years), especially smoking before first birth (1.18; 1.10-1.27 for every increase of 20 pack-years). Conversely, the direction of the association between postmenopausal smoking and BC was inverse (0.93; 0.85-1.02 for every increase of 20 pack-years). Passive smoking in childhood or adulthood was not associated with BC risk. CONCLUSION Active smoking, especially smoking before the first birth, may be associated with a modest increase in the risk of BC.
Edge shape pattern for background modeling based on hybrid local codes

In this paper, we propose a novel edge descriptor method for background modeling. In comparison to previous edge-based local-pattern methods, it is more robust to noise and illumination variations due to the use of principal gradient information in a local neighborhood. For the background modeling problem, we combined the proposed method with the Local Hybrid Pattern and experimented with an adaptive-dictionary-model based background modeling method. We show in the quantitative evaluations that the proposed methods is better than other local edge descriptors when applied to the same framework. Furthermore, we show that our proposed method is more powerful than other state of the art methods on standard datasets for the background modeling problem.
Extracting Plant Phenology Metrics in a Great Basin Watershed: Methods and Considerations for Quantifying Phenophases in a Cold Desert

Plant phenology is recognized as important for ecological dynamics. There has been a recent advent of phenology and camera networks worldwide. The established PhenoCam Network has sites in the United States, including the western states. However, there is a paucity of published research from semi-arid regions. In this study, we demonstrate the utility of camera-based repeat digital imagery and use of R statistical phenopix package to quantify plant phenology and phenophases in four plant communities in the semi-arid cold desert region of the Great Basin. We developed an automated variable snow/night filter for removing ephemeral snow events, which allowed fitting of phenophases with a double logistic algorithm. We were able to detect low amplitude seasonal variation in pinyon and juniper canopies and sagebrush steppe, and characterize wet and mesic meadows in area-averaged analyses. We used individual pixel-based spatial analyses to separate sagebrush shrub canopy pixels from interspace by determining differences in phenophases of sagebrush relative to interspace. The ability to monitor plant phenology with camera-based images fills spatial and temporal gaps in remotely sensed data and field based surveys, allowing species level relationships between environmental variables and phenology to be developed on a fine time scale thus providing powerful new tools for land management.
Protecting lemurs: ecotourism.

In their Policy Forum “Averting lemur extinctions amid Madagascar's political crisis” (21 February, p. [842][1]), C. Schwitzer et al. call for ecotourism, community reserves, and research stations as tools for lemur conservation. In fact, ecotourism already generates net conservation gains for
VARIABLE PREDATION REGIMES PREDICT THE EVOLUTION OF SEXUAL DIMORPHISM IN A POPULATION OF THREESPINE STICKLEBACK

Abstract Sexual dimorphism is widespread in nature and can be influenced by sex-specific natural selection resulting from ecological differences between the sexes. Here we show that contrasting life-history pressures and temporal shifts in ecology can exert a strong influence on the evolution of sexual dimorphism. The bony spines exhibited by stickleback are a defense against open-water avian predators but may be detrimental against benthic macroinvertebrate predators. Female stickleback from a coastal lake in western Canada occupy a more open-water ecological niche and exhibit greater dorsal and pelvic spine number than males, but the magnitude of these differences varies among life-history stages, seasons, and years. Ecological data on diet and parasite load and 62 seasonal estimates of selection over a 15-year period show that selection favors increased spine number in females and decreased spine number in males, but only when pronounced ecological differences between the sexes results in differential exposure to the two, divergent predation regimes. Thus occasional sex-reversals in ecological niche reversed the mode of selection. These processes caused a predictable response in the subsequent generation, indicating that divergent predation caused evolutionary change in dimorphism. However, temporal oscillations in sex-specific selection resulted in no net change in sexual dimorphism over the 15-year study period, indicating that fluctuations in directional selection can be responsible for long-term stasis. Replicated shifts in selective regime can demonstrate the primacy of ecological processes in driving evolution and our results illustrate how such shifts are detectable using long-term monitoring of natural populations.
Aalborg Universitet Three-minute SPECT / CT is sufficient for the assessment of bone metastasis as add-on to planar bone scintigraphy

Background: The aim of this study is to assess whether ultra-fast acquisition SPECT/CT (UF-SPECT/CT) can replace standard SPECT/CT (std-SPECT/CT) as “add-on” to whole-body bone scintigraphy (WB-BS) for the investigation of bone metastases. Consecutive cancer patients referred for WB-BS who underwent SPECT/CT in addition to WB-BS were included. Std-SPECT, UF-SPECT, and low-dose CT were performed (std-SPECT: matrix 128 × 128, zoom factor 1, 20 s/view, 32 views; UF-SPECT: identical parameters except for 10 s/view and 16 views, reducing the acquisition time from 11 to 3 min). A consensus diagnosis was reached by two observers for each set of images (WB-BS + standard SPECT/CT or WB-BS + UF-SPECT/CT) using a three-category evaluation scale: M0: no bone metastases; M1: bone metastases; and Me: equivocal findings. Results: Among the 104 included patients, most presented with prostate cancer (n = 71) or breast cancer (n = 28). Using WB-BS + std-SPECT/CT, 71 (68%) patients were classified as M0, 19 (18%) as M1, and 14 (14%) as Me. Excellent agreement was observed between WB-BS + std-SPECT/CT and WB-BS + UF-SPECT/CT using the three-category scale: kappa = 0.91 (95% CI 0.84–0.97). No difference in observer agreement between cancer types was detected. SPECT/CT provided a definitive classification in 90 of 104 cases in which WB-BS was not entirely diagnostic. Conclusions: To investigate potential bone metastases, UF-SPECT/CT can be conducted as add-on to WB-BS to notably reduce the SPECT acquisition time without compromising diagnostic confidence.