Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical evaluation of cryosurgery in the treatment of primary liver cancer Report of 60 Cases

Cryosurgery with liquid nitrogen was employed for the treatment of 60 patients with primary liver cancer (PLC) at the Liver Cancer Research Unit, Zhong Shan Hospital, Shanghai Medical University, the People's Republic of China, from November 1973 to August 1987. Of 60 patients, subclinical stage amounted to 35% (21/60), moderate stage 55% (33/60) and late stage 10% (6/60). There were 21 cases with small PLC (⩽5 cm). The postoperative course was uneventful in all of the 60 patients. These was no operative mortality, and there was no complications such as rupture of tumor, secondary bleeding, bile leakage, or abdominal infection. The 1‐year, 2‐year, 3‐year, 4‐year, and 5‐year survival rates were 51.7% (30/58), 33.9% (19/56), 20.8% (11/53), 15.6% (7/45), and 11.4% (5/44), respectively, for the whole series. Among the 21 patients with tumor nodules ⩽5 cm in diameter, the 1‐year, 2‐year, 3‐year, 4‐year, and 5‐year survival rates were 76.2% (16/21), 61.9% (13/21), 50.0% (9/18), 41.2% (7/17), and 37.5% (6/16), respectively. These results indicate that hepatic cryosurgery is a promising, safe, and simple treatment for neoplastic disease of liver. Cryosurgery with liquid nitrogen can be considered the surgery of choice for nonresectable PLC in patients without jaundice, ascites, and noncompensated liver function, and the whole tumor mass can be involved in the frozen area.
Noninvasive measurement of blood volume in hemodialysis patients.

I t has been suggested that circulating blood volume (V) In hemodialysis (HD) patients can be estimated from the rate of change of relative blood volume recordings that is caused by a step change in ultraflitration rates (UFR). First described by Schallenberg et al. ( 1 ), this approach gave inconsistent results that then were already attributed to the limitations of the single-compartment blood volume model assumption. Recently, the approach has been revisited using newly developed on-line techniques, and results have also been compared with data obtained from Isotope dilution experiments (2,3). We analyzed the technique and tested the hypothesis regarding whether the relative difference between subsequent V measurements performed during the same HD treatment compared with the amount of relative blood volume changes that had occurred between measurements as calculated from hematocrit (hct), plasma protein (PPC), and total blood protein concentration (TPC) values.
In vitro evaluation of the antimicrobial activity of nanosilver-mineral trioxide aggregate against frequent anaerobic oral pathogens by a membrane-enclosed immersion test

Background: Nanoparticles of silver (NanoAg) have been shown to control the growth of bacteria, but application of NanoAg in endodontics has not been evaluated. This in vitro study evaluates the antimicrobial activity of NanoAg to enhance the inhibitory effects of mineral trioxide aggregate (MTA). Methods: The antibacterial activities of NanoAg and NanoAg-MTA against four types of anaerobic pathogens were tested in vitro using (1) agar diffusion test (ADT) and (2) a newly devised membrane-enclosed immersion test (MEIT). Results: Both NanoAg and NanoAg-MTA inhibited the growth of all four test bacteria at 25 ppm concentration. MEIT analysis consistently showed that NanoAg enhanced the antimicrobial activity of MTA significantly, and the bacterial susceptibility to lower concentrations of NanoAg varied depending on the type of bacteria. Overall, NanoAg-MTA showed significant inhibitory effect which was time and dose dependent. Conclusions: Our data support that NanoAg can serve as an excellent MTA additive against anaerobic endodontic-periodontal pathogens with clinical applications for infection control in endodontics.
Mechanical effects of EB1 on microtubules depend on GTP hydrolysis state and presence of paclitaxel

Using the nonhydrolyzable GTP analog GMPCPP and the slowly hydrolyzable GTPγS, we polymerize microtubules that recapitulate the end binding behavior of the plus end interacting protein (+TIP) EB1 along their entire length, and use these to investigate the impact of EB1 binding on microtubule mechanics. To measure the stiffness of single filaments, we use a spectral analysis method to determine the ensemble of shapes adopted by a freely diffusing, fluorescently labeled microtubule. We find that the presence of EB1 can stiffen microtubules in a manner that depends on the hydrolysis state of the tubulin‐bound nucleotide, as well as the presence of the small‐molecule stabilizer paclitaxel. We find that the magnitude of the EB1‐induced stiffening is not proportional to the EB1‐microtubule binding affinity, suggesting that the stiffening effect does not arise purely from an increase in the total amount of bound EB1. Additionally, we find that EB1 binds cooperatively to microtubules in manner that depends on tubulin‐bound nucleotide state. © 2014 Wiley Periodicals, Inc.
Proteome Analysis of DNA Damage-induced Neuronal Death Using High Throughput Mass Spectrometry*

Isotope-coded affinity tag reagents and high throughput mass spectrometry were used to quantitate changes in the expression of 150 proteins in mouse wild-type (p53+/+) cortical neurons undergoing DNA damage-induced death. Immunological techniques confirmed several of the changes in protein expression, but microarray analysis indicated that many of these changes were not accompanied by altered mRNA expression. Proteome analysis revealed perturbations in mitochondrial function, free radical production, and neuritogenesis that were not observed in p53-deficient neurons. Changes in Tau, cofilin, and other proteins recapitulated abnormalities observed in neurodegenerative states in vivo. Additionally, DNA damage caused a p53-dependent decrease in expression of members of the protein kinase A (PKA) signaling pathway. PKA inhibition promoted death in the absence of DNA damage, revealing a novel mechanism by which endogenous down-regulation of PKA signaling may contribute to p53-dependent neuronal death. These data demonstrate the power of high throughput mass spectrometry for quantitative analysis of the neuronal proteome.
Levels of amphotericin B lipid formulations in ascites.

1. Hench LL, Splinter RJ, Allen WC et al. Bonding mechanisms at the interface of ceramic prosthetic materials. J Biomed Mater Res Symp 1971; 36: 117–41. 2. Hench LL. The story of Bioglass. J Mater Sci Mater Med 2006; 17: 967–78. 3. Peltola M, Suonpaa J, Aitasalo K et al. Obliteration of the frontal sinus cavity with bioactive glass. Head Neck 1998; 20: 315–9. 4. Stoor P, Soderling E, Salonen JI. Antibacterial effects of a bioactive glass paste on oral microorganisms. Acta Odontol Scand 1998; 56: 161–5. 5. Allan I, Newman H, Wilson M. Antibacterial activity of particulate bioglass against supraand subgingival bacteria. Biomaterials 2001; 22: 1683–7.
Scenario MPC for linear time-varying systems with individual chance constraints

This paper presents a practicable Scenario-Based Model Predictive Control (Scenario MPC) approach for linear, time-varying systems with additive disturbances. Robust MPC propagates uncertainty through the dynamics based on uncertainty sets and Stochastic MPC by multi-variable convolutions of probability distributions. The idea of Scenario MPC is to propagate the uncertainty by using sampled uncertainty scenarios. This approach is computationally efficient and (implicitly) accounts for the probabilistic distribution of disturbances. Moreover, there exists a mathematical connection between the violation rate of individual chance constraints over time and the required sample size. The theory builds on very recent results in scenario-based optimization for multi-stage stochastic decision problems. In many applications, Scenario MPC requires only a very small sample size (generally a few tens of samples). This fact is demonstrated for a large-scale example of supply chain management, for which Scenario MPC yields a good control performance.
Multi-Sender Disclosure of Verifiable Information ∗

Does competition promote disclosure? We study a class of disclosure games with multiple senders. Senders have linear preferences over a receiver’s posterior expectation of some state of the world, and conditional on the true state, each sender may draw an independent verifiable signal. We show that senders’ disclosure behavior are strategic complements when there is a cost to concealing information but strategic substitutes when there is a cost to disclosing information. Thus, when concealing information is costly, additional senders can only help a receiver; by contrast, when disclosure is costly, a receiver can be better off with fewer senders, less informed senders, or when senders face higher disclosure costs. These insights are derived from the following general result: when two Bayesian individuals have mutually-known different priors over the state, under suitable conditions, each believes that a more informative experiment (Blackwell, 1953) will, on expectation, bring the other’s posterior expectation closer to his own prior expectation. Preliminary and Incomplete. Please do not circulate without permission. ∗Together with its companion paper (Kartik, Suen, and Xu, 2014), this manuscript supersedes an earlier working paper of Xu and Suen, “Investment in Concealable Information by Competing Experts”. We thank Nageeb Ali, Tri Vi Dang, Alessandro Lizzeri, Steve Matthews, Ariel Pakes, Andrea Prat, Mike Riordan, Satoru Takahashi, Jidong Zhou, and various seminar and conference audiences for comments. We are grateful to Enrico Zanardo for alerting us to a gap in a proof in an earlier draft. Sarba Raj Bartaula and Teck Yong Tan provided excellent research assistance. †Department of Economics, Columbia University. Email: nkartik@columbia.edu. ‡School of Economics and Finance, The University of Hong Kong. Email: wsuen@econ.hku.hk. §School of Economics and Finance, The University of Hong Kong. Email: zfxu@hku.hk.
APOBEC3 Inhibition of Mouse Mammary Tumor Virus Infection: the Role of Cytidine Deamination versus Inhibition of Reverse Transcription

ABSTRACT The apolipoprotein B editing complex 3 (APOBEC3) family of proteins is a group of intrinsic antiviral factors active against a number of retroviral pathogens, including HIV in humans and mouse mammary tumor virus (MMTV) in mice. APOBEC3 restricts its viral targets through cytidine deamination of viral DNA during reverse transcription or via deaminase-independent means. Here, we used virions from the mammary tissue of MMTV-infected inbred wild-type mice with different allelic APOBEC3 variants (APOBEC3BALB and APOBEC3BL/6) and knockout mice to determine whether cytidine deamination was important for APOBEC3's anti-MMTV activity. First, using anti-murine APOBEC3 antiserum, we showed that both APOBEC3 allelic variants are packaged into the cores of milk-borne virions produced in vivo. Next, using an in vitro deamination assay, we determined that virion-packaged APOBEC3 retains its deamination activity and that allelic differences in APOBEC3 affect the sequence specificity. In spite of this in vitro activity, cytidine deamination by virion-packaged APOBEC3 of MMTV early reverse transcription DNA occurred only at low levels. Instead, the major means by which in vivo virion-packaged APOBEC3 restricted virus was through inhibition of early reverse transcription in both cell-free virions and in vitro infection assays. Moreover, the different wild-type alleles varied in their ability to inhibit this step. Our data suggest that while APOBEC3-mediated cytidine deamination of MMTV may occur, it is not the major means by which APOBEC3 restricts MMTV infection in vivo. This may reflect the long-term coexistence of MMTV and APOBEC3 in mice.
Protein phosphatase 2Cα inhibits the human stress‐responsive p38 and JNK MAPK pathways

MAPK (mitogen‐activated protein kinase) cascades are common eukaryotic signaling modules that consist of a MAPK, a MAPK kinase (MAPKK) and a MAPKK kinase (MAPKKK). Because phosphorylation is essential for the activation of both MAPKKs and MAPKs, protein phosphatases are likely to be important regulators of signaling through MAPK cascades. To identify protein phosphatases that negatively regulate the stress‐responsive p38 and JNK MAPK cascades, we screened human cDNA libraries for genes that down‐regulated the yeast HOG1 MAPK pathway, which shares similarities with the p38 and JNK pathways, using a hyperactivating yeast mutant. In this screen, the human protein phosphatase type 2Cα (PP2Cα) was found to negatively regulate the HOG1 pathway in yeast. Moreover, when expressed in mammalian cells, PP2Cα inhibited the activation of the p38 and JNK cascades induced by environmental stresses. Both in vivo and in vitro observations indicated that PP2Cα dephosphorylated and inactivated MAPKKs (MKK6 and SEK1) and a MAPK (p38) in the stress‐responsive MAPK cascades. Furthermore, a direct interaction of PP2Cα and p38 was demonstrated by a co‐immunoprecipitation assay. This interaction was observed only when cells were stimulated with stresses or when a catalytically inactive PP2Cα mutant was used, suggesting that only the phosphorylated form of p38 interacts with PP2Cα.
The effect of stimulation on the myoelectrical activity of the rectosigmoid in man

The myoelectrical activity of the rectosigmoid has been studied in 66 subjects at rest and after stimulation with either pentagastrin 6·0 μg/kg hr intravenously in 21 cases, neostigmine 0·5 mg intramuscularly in 20 cases, or two bisacodyl suppositories in 19 cases. Two electrical rhythms were present at rest. A faster rhythm (frequency 6-9 cycles/min) predominated and its incidence was significantly increased by neostigmine at all levels in the rectosigmoid and by bisacodyl in the rectum only. The incidence of the slower rhythm (frequency 2·5-4·0 cycles/min) was significantly increased by pentagastrin which had no effect on the faster rhythm. The amplitude of each basic electrical rhythm rose when its incidence was increased. Motor waves were augmented corresponding to which of the two electrical rhythms was increased after stimulation.
Large Scale Acquisition of Paraphrases for Learning Surface Patterns

Paraphrases have proved to be useful in many applications, including Machine Translation, Question Answering, Summarization, and Information Retrieval. Paraphrase acquisition methods that use a single monolingual corpus often produce only syntactic paraphrases. We present a method for obtaining surface paraphrases, using a 150GB (25 billion words) monolingual corpus. Our method achieves an accuracy of around 70% on the paraphrase acquisition task. We further show that we can use these paraphrases to generate surface patterns for relation extraction. Our patterns are much more precise than those obtained by using a state of the art baseline and can extract relations with more than 80% precision for each of the test relations.
Visual Semantic Search: Retrieving Videos via Complex Textual Queries

In this paper, we tackle the problem of retrieving videos using complex natural language queries. Towards this goal, we first parse the sentential descriptions into a semantic graph, which is then matched to visual concepts using a generalized bipartite matching algorithm. Our approach exploits object appearance, motion and spatial relations, and learns the importance of each term using structure prediction. We demonstrate the effectiveness of our approach on a new dataset designed for semantic search in the context of autonomous driving, which exhibits complex and highly dynamic scenes with many objects. We show that our approach is able to locate a major portion of the objects described in the query with high accuracy, and improve the relevance in video retrieval.
Innate Immune Responses to Bacterial Ligands in the Peripheral Human Lung – Role of Alveolar Epithelial TLR Expression and Signalling

It is widely believed that the alveolar epithelium is unresponsive to LPS, in the absence of serum, due to low expression of TLR4 and CD14. Furthermore, the responsiveness of the epithelium to TLR-2 ligands is also poorly understood. We hypothesised that human alveolar type I (ATI) and type II (ATII) epithelial cells were responsive to TLR2 and TLR4 ligands (MALP-2 and LPS respectively), expressed the necessary TLRs and co-receptors (CD14 and MD2) and released distinct profiles of cytokines via differential activation of MAP kinases. Primary ATII cells and alveolar macrophages and an immortalised ATI cell line (TT1) elicited CD14 and MD2-dependent responses to LPS which did not require the addition of exogenous soluble CD14. TT1 and primary ATII cells expressed CD14 whereas A549 cells did not, as confirmed by flow cytometry. Following LPS and MALP-2 exposure, macrophages and ATII cells released significant amounts of TNFα, IL-8 and MCP-1 whereas TT1 cells only released IL-8 and MCP-1. P38, ERK and JNK were involved in MALP-2 and LPS-induced cytokine release from all three cell types. However, ERK and JNK were significantly more important than p38 in cytokine release from macrophages whereas all three were similarly involved in LPS-induced mediator release from TT1 cells. In ATII cells, JNK was significantly more important than p38 and ERK in LPS-induced MCP-1 release. MALP-2 and LPS exposure stimulated TLR4 protein expression in all three cell types; significantly more so in ATII cells than macrophages and TT1 cells. In conclusion, this is the first study describing the expression of CD14 on, and TLR2 and 4 signalling in, primary human ATII cells and ATI cells; suggesting that differential activation of MAP kinases, cytokine secretion and TLR4 expression by the alveolar epithelium and macrophages is important in orchestrating a co-ordinated response to inhaled pathogens.
Structure-activity relationship of carbacephalosporins and cephalosporins: antibacterial activity and interaction with the intestinal proton-dependent dipeptide transport carrier of Caco-2 cells

An intestinal proton-dependent peptide transporter located on the lumenal surface of the enterocyte is responsible for the uptake of many orally absorbed beta-lactam antibiotics. Both cephalexin and loracarbef are transported by this mechanism into the human intestinal Caco-2 cell line. Forty-seven analogs of the carbacephalosporin loracarbef and the cephalosporin cephalexin were prepared to evaluate the structural features necessary for uptake by this transport carrier. Compounds were evaluated for their antibacterial activities and for their ability to inhibit 1 mM cephalexin uptake and, subsequently, uptake into Caco-2 cells. Three clinically evaluated orally absorbed carbacephems were taken up by Caco-2 cells, consistent with their excellent bioavailability in humans. Although the carrier preferred the L stereoisomer, these compounds lacked antibacterial activity and were hydrolyzed intracellularly in Caco-2 cells. Compounds modified at the 3 position of cephalexin and loracarbef with a cyclopropyl or a trifluoromethyl group inhibited cephalexin uptake. Analogs with lipophilic groups on the primary amine of the side chain inhibited cephalexin uptake, retained activity against gram-positive bacteria but lost activity against gram-negative bacteria. Substitution of the phenylglycl side chain with phenylacetyl side chains gave similar results. Compounds which lacked an aromatic ring in the side chain inhibited cephalexin uptake but lost all antibacterial activity. Thus, the phenylglycl side chain is not absolutely required for uptake. Different structural features are required for antibacterial activity and for being a substrate of the transporter. Competition studies with cephalexin indicate that human intestinal Caco-2 cells may be a useful model system for initially guiding structure-activity relationships for the rational design of new oral agents.
Algorithms for distributional and adversarial pipelined filter ordering problems

Pipelined filter ordering is a central problem in database query optimization. The problem is to determine the optimal order in which to apply a given set of commutative filters (predicates) to a set of elements (the tuples of a relation), so as to find, as efficiently as possible, the tuples that satisfy all of the filters. Optimization of pipelined filter ordering has recently received renewed attention in the context of environments such as the Web, continuous high-speed data streams, and sensor networks. Pipelined filter ordering problems are also studied in areas such as fault detection and machine learning under names such as learning with attribute costs, minimum-sum set cover, and satisficing search. We present algorithms for two natural extensions of the classical pipelined filter ordering problem: (1) a distributional-type problem where the filters run in parallel and the goal is to maximize throughput, and (2) an adversarial-type problem where the goal is to minimize the expected value of multiplicative regret. We present two related algorithms for solving (1), both running in time O(n2), which improve on the O(n3 log n) algorithm of Kodialam. We use techniques from our algorithms for (1) to obtain an algorithm for (2).
Differential Binding of Tropane-Based Photoaffinity Ligands on the Dopamine Transporter

Benztropine and its analogs are tropane ring–containing dopamine uptake inhibitors that produce behavioral effects markedly different from cocaine and other dopamine transporter blockers. We investigated the benztropine binding site on dopamine transporters by covalently attaching a benztropine-based photoaffinity ligand, [125I]N-[n-butyl-4-(4‴-azido-3‴-iodophenyl)]-4′,4"-difluoro-3α-(diphenylmethoxy)tropane ([125I]GA II 34), to the protein, followed by proteolytic and immunological peptide mapping. The maps were compared with those obtained for dopamine transporters photoaffinity labeled with a GBR 12935 analog, [125I]1-[2-(diphenylmethoxy)ethyl]-4-[2-(4-azido-3-iodophenyl)ethyl]piperazine ([125I]DEEP), and a cocaine analog, [125I]3β-(p-chlorophenyl)tropane-2β-carboxylic acid, 4′-azido-3′-iodophenylethyl ester ([125I]RTI 82), which have been shown previously to interact with different regions of the primary sequence of the protein. [125I]GA II 34 became incorporated in a membrane-bound, 14 kDa fragment predicted to contain transmembrane domains 1 and 2. This is the same region of the protein that binds [125I]DEEP, whereas the binding site for [125I]RTI 82 occurs closer to the C terminal in a domain containing transmembrane helices 4–7. Thus, although benztropine and cocaine both contain tropane rings, their binding sites are distinct, suggesting that dopamine transport inhibition may occur by different mechanisms. These results support previously derived structure–activity relationships suggesting that benztropine and cocaine analogs bind to different domains on the dopamine transporter. These differing molecular interactions may lead to the distinctive behavioral profiles of these compounds in animal models of drug abuse and indicate promise for the development of benztropine-based molecules for cocaine substitution therapies.