Miracle-dz/UniFAR-FTUs huggingface dataset:
FK506-Binding Protein 22 from a Psychrophilic Bacterium, a Cold Shock-Inducible Peptidyl Prolyl Isomerase with the Ability to Assist in Protein Folding

Adaptation of microorganisms to low temperatures remains to be fully elucidated. It has been previously reported that peptidyl prolyl cis-trans isomerases (PPIases) are involved in cold adaptation of various microorganisms whether they are hyperthermophiles, mesophiles or phsycrophiles. The rate of cis-trans isomerization at low temperatures is much slower than that at higher temperatures and may cause problems in protein folding. However, the mechanisms by which PPIases are involved in cold adaptation remain unclear. Here we used FK506-binding protein 22, a cold shock protein from the psychrophilic bacterium Shewanella sp. SIB1 (SIB1 FKBP22) as a model protein to decipher the involvement of PPIases in cold adaptation. SIB1 FKBP22 is homodimer that assumes a V-shaped structure based on a tertiary model. Each monomer consists of an N-domain responsible for dimerization and a C-catalytic domain. SIB1 FKBP22 is a typical cold-adapted enzyme as indicated by the increase of catalytic efficiency at low temperatures, the downward shift in optimal temperature of activity and the reduction in the conformational stability. SIB1 FKBP22 is considered as foldase and chaperone based on its ability to catalyze refolding of a cis-proline containing protein and bind to a folding intermediate protein, respectively. The foldase and chaperone activites of SIB1 FKBP22 are thought to be important for cold adaptation of Shewanella sp. SIB1. These activities are also employed by other PPIases for being involved in cold adaptation of various microorganisms. Despite other biological roles of PPIases, we proposed that foldase and chaperone activities of PPIases are the main requirement for overcoming the cold-stress problem in microorganisms due to folding of proteins.
A multi-hop QoS assurance method in IEEE 802.16 mesh networks

IEEE 802.16 provides wireless broadband access approaches with support for both single-hop and multi-hop mesh modes. It defines several traffic and service categories and offers differentiated quality of service (QoS) for them through scheduling algorithms. In IEEE 802.16, a three-way handshaking mechanism is given to reserve the slots hop-by-hop for mesh networks, which is called hop-by-hop Bandwidth Reservation Protocol (HBRP). However, HBRP has large signaling overhead and longer end-to-end delay. In this paper, we provide a QoS assurance method in IEEE 802.16 Mesh networks, multi-hop bandwidth reservation Protocol (M-HBRP). After receiving MSH-DSCH. Req from its upstream node, any node in the given path will send MSH-DSCH. Req to its downstream node in the meanwhile of replying MSH-DSCH. Grant to its upstream node. The simulation results show that the M-HBRP is more effective than HBRP in the existing mesh networks at both the end-to-end delay and the throughput.
Analysis of a stochastic approximation algorithm for computing quasi-stationary distributions

Abstract We study the convergence properties of a Monte Carlo estimator proposed in the physics literature to compute the quasi-stationary distribution on a transient set of a Markov chain (see De Oliveira and Dickman (2005), (2006), and Dickman and Vidigal (2002)). Using the theory of stochastic approximations we verify the consistency of the estimator and obtain an associated central limit theorem. We provide an example showing that convergence might occur very slowly if a certain eigenvalue condition is violated. We alleviate this problem using an easy-to-implement projection step combined with averaging.
Conic Approach to Quantum Graph Parameters Using Linear Optimization Over the Completely Positive Semidefinite Cone

We investigate the completely positive semidefinite cone ${\mathcal{CS}_{+}^n}$, a new matrix cone consisting of all $n\times n$ matrices that admit a Gram representation by positive semidefinite matrices (of any size). In particular, we study relationships between this cone and the completely positive and the doubly nonnegative cone, and between its dual cone and trace positive noncommutative polynomials. We use this new cone to model quantum analogues of the classical independence and chromatic graph parameters $\alpha(G)$ and $\chi(G)$, which are roughly obtained by allowing variables to be positive semidefinite matrices instead of $0/1$ scalars in the programs defining the classical parameters. We can formulate these quantum parameters as conic linear programs over the cone ${\mathcal{CS}_{+}^n}$. Using this conic approach we can recover the bounds in terms of the theta number and define further approximations by exploiting the link to trace positive polynomials.
Expression and Self-Assembly in Baculovirus of Porcine Enteric Calicivirus Capsids into Virus-Like Particles and Their Use in an Enzyme-Linked Immunosorbent Assay for Antibody Detection in Swine

ABSTRACT Porcine enteric calicivirus (PEC) causes diarrhea and intestinal lesions in pigs. PEC strain Cowden grows to low to moderate titers in cell culture but only with the addition of intestinal contents from uninfected gnotobiotic pigs (W. T. Flynn and L. J. Saif, J. Clin. Microbiol. 26:206–212, 1988; A. V. Parwani, W. T. Flynn, K. L. Gadfield, and L. J. Saif, Arch. Virol. 120:115–122, 1991). Cloning and sequence analysis of the PEC Cowden full-length genome revealed that it is most closely related genetically to the human Sapporo-like viruses. In this study, the complete PEC capsid gene was subcloned into the plasmid pBlueBac4.5 and the recombinant baculoviruses were identified by plaque assay and PCR. The PEC capsid protein was expressed in insect (Sf9) cells inoculated with the recombinant baculoviruses, and the recombinant capsid proteins self- assembled into virus-like particles (VLPs) that were released into the cell supernatant and purified by CsCl gradient centrifugation. The PEC VLPs had the same molecular mass (58 kDa) as the native virus capsid and reacted with pig hyperimmune and convalescent-phase sera to PEC Cowden in enzyme-linked immunosorbent assay (ELISA) and Western blotting. The PEC capsid VLPs were morphologically and antigenically similar to the native virus by immune electron microscopy. High titers (1:102,400 to 204,800) of PEC-specific antibodies were induced in guinea pigs inoculated with PEC VLPs, suggesting that the VLPs could be useful for future candidate PEC vaccines. A fixed-cell ELISA and VLP ELISA were developed to detect PEC serum antibodies in pigs. For the fixed-cell ELISA, Sf9 cells were infected with recombinant baculoviruses expressing PEC capsids, followed by cell fixation with formalin. For the VLP ELISA, the VLPs were used for the coating antigen. Our data indicate that both tests were rapid, specific, and reproducible and might be used for large-scale serological investigations of PEC antibodies in swine.
Self-consistent first-principles technique with linear scaling.

An algorithm for first-principles electronic structure calculations having a computational cost which scales linearly with the system size is presented. Our method exploits the real-space localization of the density matrix, and in this respect it is related to the technique of Li, Nunes and Vanderbilt. The density matrix is expressed in terms of localized support functions, and a matrix of variational parameters, L, having a finite spatial range. The total energy is minimized with respect to both the support functions and the elements of the L matrix. The method is variational, and becomes exact as the ranges of the support functions and the L matrix are increased. We have tested the method on crystalline silicon systems containing up to 216 atoms, and we discuss some of these results.
Assessment of five-year experience with abdominal organ cluster transplantation.

BACKGROUND Upper abdominal exenteration (resection of the liver, stomach, spleen, pancreaticoduodenal complex, and part of the colon) for the treatment of otherwise unresectable tumors is one of the more radical operations in oncology. This study was done to analyze retrospectively a five-year experience with exenteration in 57 patients treated with variations of resectional and transplant reconstructive techniques. STUDY DESIGN Sixty-one transplantations were performed upon 57 patients. Three different organ replacement techniques were used: liver-pancreas-duodenum en bloc (original procedure), liver only (modified procedure), and liver plus pancreatic islets. The diagnoses were cholangiocarcinoma (20 patients), hepatocellular carcinoma (12 patients), endocrine neoplasms (14 patients), sarcoma (six patients), and adenocarcinoma of the pancreas (two patients), colon (two patients), or gallbladder (one patient). Analyses of survival and tumor recurrence were stratified by procedure variations, type and extent of tumor, and immunosuppressive regimen. RESULTS The three month and one, two, three, and five year actuarial patient survival rates were 82, 56, 38, 33, and 30 percent, respectively. Eighteen (31.5 percent) of the 57 patients are alive after 425 15 (standard deviation) months (range of 17 to 61 months) and 12 patients are tumor free. The actuarial survival rates stratified by transplantation procedure, immunosuppression, and tumor diagnosis and extent showed no statistically significant differences beyond the three different transplantation groups. Endocrine tumors had a better three-year survival rate (64 percent) than sarcoma (44 percent), hepatocellular carcinoma (25 percent), cholangiocarcinoma (20 percent), and the other adenocarcinomas (20 percent). Twenty-three patients (40 percent) died as a result of tumor recurrence. Patients with combined factors of no lymph node involvement, absence of vascular invasion, and metastases to the liver only (11 patients) had the lowest incidence of recurrence (27 compared to 73.5 percent, p = 0.006). CONCLUSIONS Patients with unresectable endocrine neoplasms, fibrolamellar hepatocellular carcinoma, and selected cholangiocarcinoma confined to the liver can benefit from this radical operative approach. Patients with sarcoma can achieve long survival periods but have a high recurrence rate.
Phase I trial of subcutaneous interleukin 3 in patients with refractory malignancy: hematological, immunological, and pharmacodynamic findings.

We conducted a Phase I trial of s.c. recombinant human interleukin 3 (rhIL-3) to evaluate the toxicity, maximal tolerated dose, pharmacokinetics, and in vivo biological effects of this cytokine. Thirty-one patients with refractory cancer were entered into the study between November 1991 and June 1993. Therapy consisted of s.c. rhIL-3 daily for 15 days administered to cohorts of three to nine patients at dose levels of 60-4000 microgram/m2/day. Cycles were repeated at intervals of 28 days. Seventy-five cycles of rhIL-3 were administered (median, two per patient) and the maximal tolerated dose was 2000 microgram/m2/day. Toxicity was moderate, with most patients developing chills, fever, and myalgia. Dose-limiting toxicity consisted of diarrhea (two patients) and headache (one patient). Hematological effects of rhIL-3 included significant dose-related increases of WBC (P < 0.001), neutrophils (P < 0.001), and eosinophils (P < 0.001). Platelet counts and absolute lymphocyte numbers also increased. Various CD3(+) lymphocyte subsets increased; however, lytic activity (natural killer and lymphokine-activated killer) of peripheral blood lymphocytes was not enhanced. Serum levels of the soluble IL-2 receptor increased in a dose-related fashion, and IL-2-induced lymphocyte proliferation also was increased variably. Pharmacokinetic studies were performed in 13 patients, and area under the curve and maximal concentration values increased with increasing rhIL-3 dose levels (P < 0.001) and correlated with maximal changes from baseline in WBC, neutrophils, and eosinophils. rhIL-3 antibodies were detected in 8% of patients by day 29 of cycle 1 but were not neutralizing. rhIL-3 is well tolerated when administered s.c. and has reproducible hematological and immunological effects. The pleiotropic effects of this cytokine on various in vivo biological parameters were demonstrated clearly. Further studies of its immunoregulatory effects are warranted.
Knowledge Assets and Firm Performance: An Empirical Approach Examining the Causal Ambiguity Paradox

In the new economy, the sustainable competitive advantage of business firms flows from the creation, ownership, protection and use of difficult-to-imitate commercial and industrial knowledge assets. Such assets include tacit and codified know-how, both technical and organizational. Competitive advantage undergirded by such assets can be sustainable to the extent to which it is transferable and useable inside the firm, but difficult for outsiders to access and/or recreate. Knowledge management can be used to describe the plethora of procedures and techniques used to get the most from a firm’s knowledge assets. Resource-based theory argues that resources must be valuable, rare, inimitable, and lack substitutes to confer competitive advantage. Although scholars recognize a positive relationship between causal ambiguity and inimitability, the relationship among critical resources called competencies, causal ambiguity, and firm performance remains an unresolved conundrum. This paper takes a resource-based view to develop and test hypotheses that relates managers’ perceptions of causal ambiguity to their firm’s performance. The hypotheses examine relationships between firm performance and (1) causal ambiguity regarding the link between competencies and competitive advantage, and (2) causally ambiguous characteristics of competencies. Research involving 105 executives in 15 organizations provides valuable insights into the relationships between causal ambiguity and firm performance. Particular consideration is given to the differing ways top and middle managers in a firm may experience causal ambiguity and to how these differences may be understood and managed.
Learning Disabilities or Difference: A Critical Look at Issues Associated with the Misidentification and Placement of Hispanic Students in Special Education Programs

A new generation of Hispanic students are at risk due to inadequacies in our educational system. The inadequacies which include lack of prepared teachers and misuse of testing and assessment procedures impact special education programs, in particular, when one examines practices relative to Latino students in the area of learning disabilities. The article addresses problems in the definition of learning disabilities, learner variability, and the effects of race, poverty, culture, and language on educational outcomes. The authors call for a new assessment paradigm that would require the restructuring of professional development programs and institutional practices in public schools that are not in line with current research on topics related to this population including second language acquisition and cognitive development.
Proportionally fair allocation of end-to-end bandwidth in STDMA wireless networks

We consider the problem of designing distributed mechanisms for joint congestion control and resource allocation in spatial-reuse TDMA wireless networks. The design problem is posed as a utility maximization subject to link rate constraints that involve both power allocation and transmission scheduling over multiple time-slots. Starting from the performance limits of a centralized optimization based on global network information,we proceed systematically in the development of distributed and transparent protocols. In the process,we introduce a novel decomposition method for convex optimization,establish its convergence for the utility maximization problem and demonstrate how it suggests a distributed solution based on flow control optimization and incremental updates of the transmission schedule.We develop a two-step procedure for finding the schedule updates and suggest two schemes for distributed channel reservation and power control under realistic interference models. Although the final protocols are suboptimal,we isolate and quantify the performance losses incurred by each simplification and demonstrate strong performance in examples.
Nominal Bonds, Real Bonds, and Equity

We decompose the term structure of expected equity returns into (1) the real short rate, (2) a premium for holding real long-term bonds, or the real duration premium, the excess returns of nominal long-term bonds over real bonds which reflects (3) expected inflation and (4) inflation risk, and (5) a real cashflow risk premium, which is the excess return of equity over nominal bonds. The shape of the nominal and real bond yield curves are upward sloping due to increasing duration and inflation risk premiums. The term structures of expected equity returns and equity risk premiums, in contrast, are downward sloping due to the decreasing effect of short-term expected inflation, or trend inflation, across horizons. Around 70% of the variation of expected equity returns at the 10-year horizon is due to variation in the output gap and trend inflation.
Strategy Synthesis in Adversarial Patrolling Games

Patrolling is one of the central problems in operational security. Formally, a patrolling problem is specified by a set $U$ of nodes (admissible defender's positions), a set $T \subseteq U$ of vulnerable targets, an admissible defender's moves over $U$, and a function which to every target assigns the time needed to complete an intrusion at it. The goal is to design an optimal strategy for a defender who is moving from node to node and aims at detecting possible intrusions at the targets. The goal of the attacker is to maximize the probability of a successful attack. We assume that the attacker is adversarial, i.e., he knows the strategy of the defender and can observe her moves. We prove that the defender has an optimal strategy for every patrolling problem. Further, we show that for every $\varepsilon$ > 0, there exists a finite-memory $\varepsilon$-optimal strategy for the defender constructible in exponential time, and we observe that such a strategy cannot be computed in polynomial time unless P=NP. Then we focus ourselves to unrestricted defender's moves. Here, a patrolling problem is fully determined by its signature, the number of targets of each attack length. We bound the maximal probability of successfully defended attacks. Then, we introduce a decomposition method which allows to split a given patrolling problem $G$ into smaller subproblems and construct a defender's strategy for $G$ by "composing" the strategies constructed for these subproblems. Finally, for patrolling problems with $T = U$ and a well-formed signature, we give an exact classification of all sufficiently connected environments where the defender can achieve the same value as in the fully connected uniform environment. This result is useful for designing "good" environments where the defender can act optimally.
Evaluation of Diurnal Variation in Fentanyl Clearance

Drug disposition kinetics are commonly assumed to be time‐invariant as a first approximation. In a preliminary study, 6 healthy volunteers received a constant intravenous infusion of 50 μg/h for 48 hours; the serum fentanyl concentration at 36 hours was lower than that at 24 hours for all 6 subjects. This suggested possible diurnal variations in fentanyl clearance. In 2 subsequent studies, with healthy volunteers receiving short infusions of fentanyl (n = 9, 150 μg/h for 0.33 hours every 4 hours; n = 12, 150 μg/h for 0.33 hours every hour, respectively), the area under the serum fentanyl concentration curve appeared to be independent of the time of infusion. Thus, there was no evidence to support a large diurnal change in fentanyl clearance. The serum fentanyl concentration‐time profiles, corrected for carryover from previous doses, within each study were superimposable. This suggests that there are no diurnal changes in the distribution kinetics of fentanyl.
Rictor in Perivascular Adipose Tissue Controls Vascular Function by Regulating Inflammatory Molecule Expression

Objective—Perivascular adipose tissue (PVAT) wraps blood vessels and modulates vasoreactivity by secretion of vasoactive molecules. Mammalian target of rapamycin complex 2 (mTORC2) has been shown to control inflammation and is expressed in adipose tissue. In this study, we investigated whether adipose-specific deletion of rictor and thereby inactivation of mTORC2 in PVAT may modulate vascular function by increasing inflammation in PVAT. Approach and Results—Rictor, an essential mTORC2 component, was deleted specifically in mouse adipose tissue (rictorad−/−). Phosphorylation of mTORC2 downstream target Akt at Serine 473 was reduced in PVAT from rictorad−/− mice but unaffected in aortic tissue. Ex vivo functional analysis of thoracic aortae revealed increased contractions and impaired dilation in rings with PVAT from rictorad−/− mice. Adipose rictor knockout increased gene expression and protein release of interleukin-6, macrophage inflammatory protein-1&agr;, and tumor necrosis factor-&agr; in PVAT as shown by quantitative real-time polymerase chain reaction and Bioplex analysis for the cytokines in the conditioned media, respectively. Moreover, gene and protein expression of inducible nitric oxide synthase was upregulated without affecting macrophage infiltration in PVAT from rictorad−/− mice. Inhibition of inducible nitric oxide synthase normalized vascular reactivity in aortic rings from rictorad−/− mice with no effect in rictorfl/fl mice. Interestingly, in perivascular and epididymal adipose depots, high-fat diet feeding induced downregulation of rictor gene expression. Conclusions—Here, we identify mTORC2 as a critical regulator of PVAT-directed protection of normal vascular tone. Modulation of mTORC2 activity in adipose tissue may be a potential therapeutic approach for inflammation-related vascular damage.
Clinical diagnosis of Ménière's disease: how useful are the American Academy of Otolaryngology Head and Neck Surgery Committee on Hearing and Equilibrium guidelines?

Abstract Introduction: Ménière's disease is a diagnosis requiring expert clinical judgment. There are several differences between the American Academy of Otolaryngology Head and Neck Surgery diagnostic guidelines and Prosper Ménière's original description of the disease. Methods: Six hundred and fifty patients attending a specialist balance clinic had their clinical profiles fully analysed according to each set of diagnostic criteria. Results: Application of the American Academy of Otolaryngology Head and Neck Surgery guidelines resulted in the diagnosis of three times more patients than did use of Ménière's diagnostic criteria. Treatment options for patients in both groups were similar. It is unlikely that the application of different diagnostic criteria would have an effect on the treatment of individual patients. Discussion: The American Academy of Otolaryngology Head and Neck Surgery guidelines are more sensitive and less specific in diagnosing Ménière's disease than Prosper Ménière's original description. Standardised criteria should be applied across published series, in order to make results accurate, comparable and useful in the long term. We would recommend the introduction of a stricter diagnostic category for definite Ménière's disease.