Miracle-dz/UniFAR-FTUs huggingface dataset:
Matrix models for a changeable world: the importance of transient dynamics in population management

1. Matrix population models are tools for elucidating the association between demographic processes and population dynamics. A large amount of useful theory pivots on the assumption of equilibrium dynamics. The preceding transient is, however, of genuine conservation concern as it encompasses the short-term impact of natural or anthropogenic disturbance on the population. 2. We review recent theoretical advances in deterministic transient analysis of matrix projection models, considering how disturbance can alter population dynamics by provoking a new population trajectory. 3. We illustrate these impacts using plant and vertebrate systems across contiguous and fragmented landscapes. 4. Short-term responses are of fundamental relevance for applied ecology, because the time-scale of transient effects is often similar to the length of many conservation projects. Investigation of the immediate, post-disturbance phase is vital for understanding how population processes respond to widespread disturbance in the short- and into the long term. 5. Synthesis and applications. Transient analysis is critical for understanding and predicting the consequences of management activities. By considering short-term population responses to perturbations, especially in long-lived species, managers can develop more informed strategies for species harvesting or controlling of invasive species.
Photodynamic Effect of Iron Excess on Photosystem II Function in Pea Plants ¶

An earlier mechanistic phase of iron toxicity in photosynthetic cells was interpreted in terms of enhanced photodynamic action by the cytochrome b6/f complex (Cyt b6/f) via singlet oxygen (1O2) on the photosystem II complex (PS II). Iron excess was induced in hydroponically cultured pea (Pisum sativum L.) plants, and its effect on the function of PS II in vivo as well as in vitro was studied under high‐irradiance conditions. Iron excess in plants gave rise to a significant increase in Cyt b6/f content of thylakoids. It appeared that the larger the content of Cyt b6/f, the more susceptible PS II was to photoinhibition, and the higher the rate of 1O2 photoproduction in thylakoids was. The action spectrum for degradation of the D1 protein in thylakoids revealed that photosensitization by nonporphyrin chromophore(s) was apparently associated with near UV to blue light–induced deterioration of PS II. The results are pertinent to the concept that photooxidative damage to PS II, exacerbated by iron accumulation in thylakoid membranes in the form of Cyt b6/f, is involved in the mechanism of iron toxicity in leaf cells.
Effects of tube drain with primary closure technique on postoperative trismus and swelling after removal of fully impacted mandibular third molars.

OBJECTIVE Surgical removal of impacted mandibular third molars with primary wound closure may result in postoperative edema, facial swelling, pain, and restriction of mouth opening. The type of closure may be a cause of these complications. The aim of this study was to compare the effects of placement of a surgical tube drain before primary closure with the effects of primary closure alone after removal of fully impacted mandibular third molars. METHOD AND MATERIALS The study group included 13 patients aged 15 to 39 years with bilateral fully impacted mandibular third molars. The insertion of a small surgical tube drain before primary closure (drain group) was compared to a simple primary closure procedure (no drain group) after removal of the impacted third molars in a randomized crossover design. The duration of the operation was recorded. Patients were evaluated 1, 2, 3, and 7 days postoperatively for facial swelling and trismus. RESULTS The facial swelling experienced by the drain group was significantly less than that experienced by the no drain group. The degree of trismus was greater in the no drain group than in the drain group, but the difference was not statistically significant. CONCLUSION Use of a surgical drain, especially after removal of fully impacted third molars, will reduce postoperative facial swelling.
Association of epidermal growth factor receptor (EGFR) gene mutations with EGFR amplification in advanced non‐small cell lung cancer

Somatic mutations in the epidermal growth factor receptor (EGFR) gene are associated with the response to EGFR tyrosine kinase inhibitors in patients with non‐small cell lung cancer (NSCLC). Increased EGFR copy number has also been associated with sensitivity to these drugs. However, given that it is often difficult to obtain sufficient amounts of tumor tissue for genetic analysis from patients with advanced NSCLC, the relationship between these two types of EGFR alterations has remained unclear. We have now evaluated EGFR mutation status both by direct sequencing and with a high‐sensitivity assay, the Scorpion‐amplification‐refractory mutation system, and have determined EGFR copy number by fluorescence in situ hybridization (FISH) analysis in paired tumor specimens obtained from 100 consecutive patients with advanced NSCLC treated with chemotherapy. EGFR mutations or FISH positivity (EGFR amplification or high polysomy) were apparent in 18% (18/100) and 32% (32/100) of patients, respectively. The Scorpion‐amplification‐refractory mutation system was more sensitive than direct sequencing for the detection of EGFR mutations. Furthermore, EGFR mutations were associated with EGFR amplification (P = 0.009) but not with FISH positivity (P = 0.266). Our results therefore suggest the existence of a significant association between EGFR mutation and EGFR amplification in patients with advanced NSCLC. (Cancer Sci 2008; 99: 2455–2460)
Genotyping of Norovirus Strains Detected in Outbreaks between April 2002 and March 2003 in Osaka City, Japan

Noroviruses (NVs) are the major cause of food‐ and waterborne nonbacterial gastroenteritis in Japan. Between April 2002 and March 2003, a total of 111 fecal specimens from 40 outbreaks of acute nonbacterial gastroenteritis in Osaka City, Japan were subject to NV detection. Seventy‐two samples (64.9%) from 31 outbreaks (77.5%) were NV positive by a real time reverse transcription (RT)‐PCR assay. To further determine the genotype of individual NV strains, we sequenced the capsid N‐terminal/shell (N/S) domain of some representative strains from each outbreak. The 51 NV strains detected in this study were segregated into 15 genotypes (6 in genogroup I and 9 in genogroup II), and GII/5 genotype NV was a dominant outbreak genotype.
Rare Variants in Tissue Inhibitor of Metalloproteinase 2 as a Risk Factor for Schizophrenia: Evidence From Familial and Cohort Analysis

Candidate gene and genome-wide association study based common risk variant identification is being complemented by whole exome sequencing (WES)/whole genome sequencing based rare variant discovery in elucidation of genetic landscape of schizophrenia (SZ), a common neuropsychiatric disorder. WES findings of de novo mutations in case-parent trios have further implied genetic etiology, but do not explain the high genetic risk in general populations. Conversely, WES in multiplex families may be an insightful strategy for the identification of highly penetrant rare variants in SZ and possibly enhance our understanding of disease biology. In this study, we analyzed a 5-generation Indian family with multiple members affected with SZ by WES. We identified a rare heterozygous missense variant (NM_003255: c.506C>T; p.Pro169Leu; MAF = 0.0001) in Tissue Inhibitor of Metalloproteinase 2 (TIMP2, 17q25.3) segregating with all 6 affected individuals but not with unaffected members. Linkage analysis indicated a maximum logarithm of the odds score of 1.8, θ = 0 at this locus. The variant was predicted to be damaging by various in silico tools and also disrupt the structural integrity by molecular dynamics simulations. WES based screening of an independent SZ cohort (n = 370) identified 4 additional rare missense variants (p.Leu20Met, p.Ala26Ser, p.Lys48Arg and p. Ile217Leu) and a splice variant rs540397728 (NM_003255:c.232-5T>C), also predicted to be damaging, increasing the likelihood of contribution of this gene to SZ risk. Extensive biochemical and knockout mouse studies suggesting involvement of TIMP2 in neurodevelopmental and behavioral deficits, together with genetic evidence for TIMP2 conferring SZ risk from this study may have possible implications for new therapeutics.
O‐GlcNAc cycling: How a single sugar post‐translational modification is changing the Way We think about signaling networks

O‐GlcNAc is an ubiquitous post‐translational protein modification consisting of a single N‐acetlyglucosamine moiety linked to serine or threonine residues on nuclear and cytoplasmic proteins. Recent work has begun to uncover the functional roles of O‐GlcNAc in cellular processes. O‐GlcNAc modified proteins are involved in sensing the nutrient status of the surrounding cellular environment and adjusting the activity of cellular proteins accordingly. O‐GlcNAc regulates cellular responses to hormones such as insulin, initiates a protective response to stress, modulates a cell's capacity to grow and divide, and regulates gene transcription. This review will focus on recent work involving O‐GlcNAc in sensing the environment and regulating signaling cascades. © 2005 Wiley‐Liss, Inc.
sCD30 and sCD40L detection in patients with osteosarcoma, chondrosarcoma and Ewing sarcoma.

BACKGROUND Primary malignant bone tumors are heterogeneous groups of neoplasms, which affect mainly children and adolescents. The most common types are Osteosarcoma, Ewing sarcoma and chondrosarcoma. Elevation of sCD30 and sCD40L has been observed in lymphoma, leukemia and autoimmune disorders. OBJECTIVE To evaluate serum concentrations of sCD30 and sCD40L in patients with primary malignant bone tumors. METHOD Fifty-four cases (31 Osteosarcomas, 14 Ewing sarcomas, and 9 Chondrosarcomas) and 54 healthy controls enrolled in this study. Cases with the history of prior treatment (surgery, chemotherapy and radiotherapy) were excluded from the study. Serum levels of sCD30 and sCD40L were detected by an enzyme linked immunosorbent assay (ELISA). RESULTS Mean serum concentration of sCD30 in Ewing sarcoma was significantly higher than that of the control groups (p=0.007), but mean serum concentrations of sCD30 in osteosarcoma and chondrosarcoma groups were not significantly different, compared to the controls (p=0.41 and p=0.11, respectively). Mean serum concentrations of sCD40L in osteosarcoma, Ewing sarcoma and chondrosarcoma groups were significantly higher than that of the control group (p<0.0001). In addition, the mean serum level of sCD40L in chondrosarcoma patients was higher than that of both Ewing sarcoma and osteosarcoma groups (p<0.001). CONCLUSION sCD30 and sCD40L increase in primary bone tumors; however the significant of these findings for diagnosis or prognosis of these tumors needs further investigation.
An integrated split-phase dual-inverter permanent magnet motor drive and battery charger for grid-connected electric or hybrid vehicles

Multi-phase machines have some features such as reduced power electronic components rating, reduced torque ripple, and increased reliability that make them a favorable option in some applications, for instance in the area of high-power drive systems. A combined motor drive and battery charger based on a split-phase interior permanent magnet synchronous motor and dual inverters is proposed and explained in this paper. By connecting the two motor winding star points to a single-phase ac supply, it is possible to charge the battery through the inverters from a commonly available single-phase outlet. In this way, a separate battery charger is not needed. A double dq model of the motor is presented and based upon a maximum torque per ampere control strategy is used for the traction mode. To eliminate the look up table to obtain the reference value of the current q component from the torque error, a linearized version of the controller is used that is explained. The system operation in the charging mode including the equivalent circuit and inverter control is also explained. Moreover, simulation results are provided to verify the proper operation of the proposed system.
Autism Spectrum Disorder Genetics: Diverse Genes with Diverse Clinical Outcomes

AbstractThe last several years have seen unprecedented advances in deciphering the genetic etiology of autism spectrum disorders (ASDs). Heritability studies have repeatedly affirmed a contribution of genetic factors to the overall disease risk. Technical breakthroughs have enabled the search for these genetic factors via genome-wide surveys of a spectrum of potential sequence variations, from common single-nucleotide polymorphisms to essentially private chromosomal abnormalities. Studies of copy-number variation have identified significant roles for both recurrent and nonrecurrent large dosage imbalances, although they have rarely revealed the individual genes responsible. More recently, discoveries of rare point mutations and characterization of balanced chromosomal abnormalities have pinpointed individual ASD genes of relatively strong effect, including both loci with strong a priori biological relevance and those that would have otherwise been unsuspected as high-priority biological targets. Evidence has also emerged for association with many common variants, each adding a small individual contribution to ASD risk. These findings collectively provide compelling empirical data that the genetic basis of ASD is highly heterogeneous, with hundreds of genes capable of conferring varying degrees of risk, depending on their nature and the predisposing genetic alteration. Moreover, many genes that have been implicated in ASD also appear to be risk factors for related neurodevelopmental disorders, as well as for a spectrum of psychiatric phenotypes. While some ASD genes have evident functional significance, like synaptic proteins such as the SHANKs, neuroligins, and neurexins, as well as fragile x mental retardation–associated proteins, ASD genes have also been discovered that do not present a clear mechanism of specific neurodevelopmental dysfunction, such as regulators of chromatin modification and global gene expression. In its sum, the progress from genetic studies to date has been remarkable and increasingly rapid, but the interactive impact of strong-effect genetic lesions coupled with weak-effect common polymorphisms has not yet led to a unified understanding of ASD pathogenesis or explained its highly variable clinical expression. With an increasingly firm genetic foundation, the coming years will hopefully see equally rapid advances in elucidating the functional consequences of ASD genes and their interactions with environmental/experiential factors, supporting the development of rational interventions.
Melatonin Regulates the Phosphorylation of CREB in Ovine Pars Tuberalis *

This study investigated whether melatonin could modulate the phosphorylation of the calcium/cyclic AMP response‐element binding‐protein (CREB) within primary cell cultures of ovine pars tuberalis (oPT) and pars distalis (oPD). Gel shift assays confirmed the presence of nuclear factors able to alter the electrophoretic mobility of a 32P‐labelled CRE oligonucleotide. Two shifted bands were observed probably due to monomer and dimer binding to the CRE. Each band was supershifted by antisera directed against both CREB and the phosphorylated form of CREB (P‐CREB), consistent with a specific role of CREB proteins in transcriptional regulation. To study the physiological role of CREB, the nuclear immunoreactivity for P‐CREB was followed in primary cultures of oPT given different pharmacological treatments. Cells stimulated with forskolin responded with a robust time‐ and dose‐dependent increase in nuclear phospho‐CREB immunoreactivity (P‐CREB‐ir), confirming that activation of this transcription factor occurred through the cyclic AMP‐PKA pathway. Maximal stimulation was achieved within 15 min and persisted for up to 1 h. Treatment with melatonin alone did not alter basal P‐CREB‐ir levels, yet melatonin inhibited the forskolin‐induced increase in P‐CREB‐ir in a dose‐dependent manner (IC50 of between 10−10M and 10−8 M melatonin when tested against 1 μM forskolin). In contrast, in primary cultures of oPD, melatonin failed to block forskolin‐stimulated increases in either the content of cyclic AMP or the intensity of nuclear P‐CREB‐ir, confirming that the action of melatonin upon P‐CREB‐ir is tissue specific. These results demonstrate that, consistent with its inhibitory effect on the activation of PKA within oPT, melatonin prevents or reverses the phosphorylation of CREB induced by activation of the cyclic AMP signal transduction pathway. Therefore melatonin has the potential to regulate gene expression in the oPT by acting upon the CREB transcription factor. However, this paper also shows that 12‐0‐tetradecanoylphorbol‐13‐acetate (TPA) which activates PKC also leads to the phosphorylation of CREB in oPT cells, suggesting the potential involvement of other signal transduction pathways in the transcriptional regulation of these cells.
Cytologic and Histologic Findings in Women Using an IUD

The present study was undertaken to determine the source of atypical squamous metaplastic cells that are found in large numbers in smears from women with an intrauterine contraceptive device (IUD). The cytologic data are obtained from a population screening program totaling 61,151 women, of which 1401 were using an IUD. Histologic data comprise findings from curettings on removal of an IUD and scrapes from the removed IUD in 102 women. These implicate the endometrial surface epithelium as the main source of the atypical cells in cervical smears from IUD users. As this epithelial atypia frequently disappears upon removal of the IUD, conservative follow-up of women with cytologic metaplastic atypia in cervical smears during IUD use is strongly recommended.
Inguinal lymphadenitis associated with Capnocytophaga bacilli

Capnocytophaga organisms are capnophilic, gram-negative bacilli that have been associated with infections deriving from the flora of the oropharynx. We report a case of inguinal adenitis caused by Capnocytophaga species that probably represents sexual transmission of the pathogen.
Golgi inheritance in small buds of Saccharomyces cerevisiae is linked to endoplasmic reticulum inheritance

According to the cisternal maturation hypothesis, endoplasmic reticulum (ER)-derived membranes nucleate new Golgi cisternae. The yeast Saccharomyces cerevisiae offers a unique opportunity to test this idea because small buds contain both ER and Golgi structures early in the cell cycle. We previously predicted that mutants defective in ER inheritance also would show defects in Golgi inheritance. Surprisingly, studies of S. cerevisiae have not revealed the expected link between ER and Golgi inheritance. Here, we revisit this issue by generating mutant strains in which many of the small buds are devoid of detectable ER. These strains also show defects in the inheritance of both early and late Golgi cisternae. Strikingly, virtually all of the buds that lack ER also lack early Golgi cisternae. Our results fit with the idea that membranes exported from the ER coalesce with vesicles derived from existing Golgi compartments to generate new Golgi cisternae. This basic mechanism of Golgi inheritance may be conserved from yeast to vertebrate cells.
Emergent literacy in a print-rich multilingual home environment

Emergent literacy research has demonstrated that literacy development begins early in literate environment of family settings. This qualitative case study explored how literacy development in early years was enhanced in a print-rich multilingual environment. It involved 3 children from 3 families in a multilingual context. Data collection focused on emergent literacy of children and how home environment and family practice supported their literacy development. Data were collected through methodological triangulation of interviews; on-site observation of authentic interactions and literate environment; as well as an audit of home literacy resources. The data were analyzed, within and across cases, before identifying discrepancies and commonalities among participants. Three prominent themes emerged from the general research questions: (1) Quality parent-child or adult-child interaction and exchanges; (2) Immersion in language and print-rich environment; and (3) Intentional explicit instruction. In conclusion, insights gained from children’s early literacy challenges teachers and educators to think more broadly and inclusively about family literacy.
The role of the amygdala in fear and anxiety.

Converging evidence now indicates that the amygdala plays a crucial role in the development and expression of conditioned fear. Conditioned fear is a hypothetical construct used to explain the cluster of behavioral effects produced when an initially neutral stimulus is consistently paired with an aversive stimulus. For example, when a light, which initially has no behavioral effect, is paired with an aversive stimulus such as a footshock, the light alone can elicit a constellation of behaviors that are typically used to define a state of fear in animals. To explain these findings, it is generally assumed (cf. McAllister & McAllister 1971 ) that during light-shock pair­ ings (training session ), the shock elicits a variety of behaviors that can be used to infer a central state of fear (unconditioned responses-Figure 1 ). After pairing , the light can produce the same central fear state and thus the same set of bchaviors formerly produced by thc shock. Moreover, the behavioral effects that are produced in animals by this formerly neutral stimulus (now called a conditioned stimulus-CS ) are similar in many respects to the constellation of behaviors that are used to diagnose gener­ alized anxiety in humans (Table 1 ). This chapter summarizes data sup­ porting the idea that the amygdala, and its many efferent projections, may represent a central fear system involved in both the expression and acquisition of conditioned fear.
On the Role of Human Mortality in Information System Security: From the Problems of Descriptivism to Non-Descriptive Foundations

The question of whether ethical theories appealing to human morality can serve as a means of protection against information system security breaches has been recognised by several authors. The existing views concerning the role of ethics in information systems security can be divided into two categories. These are 1 expressions about the use of human morality and 2 arguments claiming that the use of ethics is useless or, at best, extremely restricted. However, the former views are general statements lacking concrete guidance and the latter viewpoint is based on cultural relativism, and can be thus classified as descriptivism. This paper claims that the use of ethical theories and human morality is useful for security, particularly given that Hare's Overriding thesis has validity-though it has its limitations, too. This paper further argues that descriptivism including the doctrine of cultural relativism leads to several problems, contradictions and causes detrimental effects to our well-being and security. Therefore, an alternative approach to using ethics in minimising security breaches that is based on non-descriptive theories is proposed. The use of non-descriptivism will be demonstrated using Rawls' concept of the "veil of ignorance. " The limitations of non-descriptivism, and appealing to human morality in a general sense, will also be discussed. Finally, suggestions for future research directions are outlined.