bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perceiving Tongue Position
Authors: Grover Cynthia , Craske Brian 
Published: January 2007

Two experiments on perceiving the tongue position were conducted in which naive human subjects pointed to gingival targets, or to extensions of their fingertip, with their tongue. The aim in experiment 1 was to inquire about the existence and accuracy of the perception of the horizontal position of the tongue inside and outside the mouth, and whether kinesthetic elements other than the skin might contribute to perceiving tongue position. Vertical positioning and the calibration of the sensory map that can be presumed to underlie position sense in the tongue were examined in experiment 2. It was found that position sense is equally good in the presence and absence of anesthesia of the mucosa, suggesting that the muscles, tendons, and corollary discharge contribute to position sense in the tongue. Perception of the tongue position both inside and outside the mouth is accurate, with the error in tongue positioning being about 2°. Feedback improved naive subjects' accuracy very little.
Factors Limiting Large-Scale Localisation
Authors: Sterken Yvonne , Toet Alexander , Yap Yen-Lee 
Published: January 2007

The mechanisms mediating relative spatial localisation in the visual system are still unclear. There is a growing amount of evidence that this capability is not merely limited by the processing of the front-end visual system. Models of localisation should, therefore, include higher-level processing stages. A careful study of the sources of error in localisation tasks may further our understanding of the nature of these processes. A study is reported in which the possible role of higher-order processing in relative spatial localisation is explicitly addressed. For this purpose the error sources of threshold performance were investigated for two similar relative-spatial-localisation tasks: two-dot separation discrimination and two-dot orientation discrimination. Fovea-centred stimuli with large dot separations were used. The front-end processing for these stimuli is probably identical in both tasks. Hence, differential effects of the variation of the experimental parameters on threshold performance for both tasks may reveal the characteristics of the higher-level processing involved. The effects of dot separation, stimulus orientation, and experimental procedure (single-stimulus binary forced choice versus two-alternative forced choice) on threshold performance for both tasks are reported. The results show that thresholds for both tasks increase proportionally with dot separation. However, separation-discrimination thresholds are always significantly higher than orientation-discrimination thresholds. Thresholds for separation discrimination are independent of stimulus orientation. In contrast, orientation-discrimination thresholds show an oblique effect: thresholds are consistently lower for horizontal stimuli. Both tasks also show a different dependency of threshold behaviour on the experimental procedure. For a horizontal stimulus orientation, separation discrimination is better with an explicit (physical) reference standard, whereas orientation discrimination is better with an implicit referent. These differential effects cannot be explained by any of the known characteristics of the front-end visual system. They suggest that large-scale spatial-localisation performance is probably limited at a processing level at which spatial relations are explicitly represented.
Visual Factors Affecting the Rod-And-Frame Illusion: Role of Gap Size and Frame Components
Authors: Antonucci Gabriella , Fanzon Daniela , Spinelli Donatella , Zoccolotti Pierluigi 
Published: January 2007

In two studies the effect of the distance between the tip of the rod and the frame sides (gap) in the rod-and-frame (RF) illusion was examined and the effect of a full-square condition was compared with that of two different frame amputations. In both studies, there were more rod-setting errors in the direction of the tilt of the inducing figure with a small gap than with a large one. These findings are consistent with the idea that in the case of small gap size local interactions contribute to determining the RF illusion. The actual length of the rod was varied in order to keep the gap constant across different frame tilts; therefore these findings cannot be due to the co-variation between gap size and frame tilt which is typical of standard apparatuses. The effect of frame amputations was compared to the full-square condition. According to Wenderoth and Beh, amputations that maintain the two orthogonal contours of the square produce the typical angular function of the RF illusion. This prediction was confirmed in both studies. However, results indicate that the full square has a stronger illusory effect in the case of a small degree of tilt of the inducing stimulus, irrespective of gap size. It is suggested that this ‘square superiority’ effect is related to global, not local, mechanisms. To pursue Wenderoth and Beh's observations, amputations close to the vertical meridian were used in one experiment and those close to the horizontal meridian in the second experiment. Contrary to predictions, these conditions produced overlapping results.
Haptic Unilateral and Bilateral Discrimination of Curved Surfaces
Authors: Kappers Astrid M L , Koenderink Jan J 
Published: January 2007

Active haptic discrimination of cylindrically curved hand-sized surfaces was investigated. Unilateral discrimination (that is, with one hand, either the left or the right one) was compared with bilateral discrimination. In this latter condition, the right hand had to touch the right surface, and the left hand the left one. The importance of which surface of the pair is placed to the right of the observer and which to the left (the so-called placement order) was also investigated. In comparison with existing studies, performance in the present experiments was better owing to the combined effects of a larger surface area and active instead of passive discrimination. The results show clearly that curvature discrimination does not follow a Weber law; performance is relatively better with the larger curvatures. For all subjects, unilateral discrimination was much better than bilateral discrimination. A partial cause of this difference is the influence of the placement order, which is very apparent in the results for the bilateral condition. These results cannot be fully explained but the findings suggest an influence of the object–observer relation on the perception of the object.
Electrostatic screening and backbone preferences of amino acid residues in urea‐denatured ubiquitin
Authors: Avbelj Franc , Grdadolnik Simona Golic 
Published: January 2007

AbstractLocal structures in denatured proteins may be important in guiding a polypeptide chain during the folding and misfolding processes. Existence of local structures in chemically denatured proteins is a highly controversial issue. NMR parameters [coupling constants 3 J(Hα,HN) and chemical shifts] of chemically denatured proteins in general deviate little from their values in small peptides. These peptides were presumed to be completely unstructured; therefore, it was considered that chemically denatured proteins are random coils. But recent experimental studies show that small peptides adopt relatively stable structures in aqueous solutions. Small deviations of the NMR parameters from their values in small peptides may thus actually indicate the existence of local structures in chemically denatured proteins. Using NMR data and theoretical predictions we show here that fluctuating β‐strands exist in urea‐denatured ubiquitin (8 M urea at pH 2). Residues in such β‐strands populate more frequently the left side of the broad β region of Φ–ψ space. Urea‐denatured ubiquitin contains no detectable β‐sheet secondary structures; nevertheless, the fluctuating β‐strands in urea‐denatured ubiquitin coincide to the β‐strands in the native state. Formation of β‐strands is in accord with the electrostatic screening model of unfolded proteins. The free energy of a residue in an unfolded protein is in this model determined by the local backbone electrostatics and its screening by backbone solvation. These energy terms introduce strong electrostatic coupling between neighboring residues, which causes cooperative formation of β‐strands in denatured proteins. We propose that fluctuating β‐strands in denatured proteins may serve as initiation sites to form fibrils.
Protein fabrication automation
Authors: Cox J. Colin , Lape Janel , Sayed Mahmood A. , Hellinga Homme W. 
Published: January 2007

AbstractFacile “writing” of DNA fragments that encode entire gene sequences potentially has widespread applications in biological analysis and engineering. Rapid writing of open reading frames (ORFs) for expressed proteins could transform protein engineering and production for protein design, synthetic biology, and structural analysis. Here we present a process, protein fabrication automation (PFA), which facilitates the rapid de novo construction of any desired ORF from oligonucleotides with low effort, high speed, and little human interaction. PFA comprises software for sequence design, data management, and the generation of instruction sets for liquid‐handling robotics, a liquid‐handling robot, a robust PCR scheme for gene assembly from synthetic oligonucleotides, and a genetic selection system to enrich correctly assembled full‐length synthetic ORFs. The process is robust and scalable.
The protease allergen Der p 1 cleaves cell surface DC‐SIGN and DC‐SIGNR: experimental analysis of in silico substrate identification and implications in allergic responses
Authors: Furmonaviciene R. , Ghaemmaghami A. M. , Boyd S. E. , Jones N. S. , Bailey K. , Willis A. C. , Sewell H. F. , Mitchell D. A. , Shakib F. 
Published: January 2007

SummaryBackground
The cysteine protease Der p 1 from the house dust mite Dermatophagoides pteronyssinus is one of the most potent allergens known. An attractive mechanism for a component of Der p 1 allergenicity lies in its ability to cleave key regulatory molecules from leucocyte surfaces, subverting cellular function and driving abnormal immunoglobulin E (IgE) responses.Objective
Although CD23, CD25 and CD40 have already been identified as major Der p 1 targets, other significant substrates may also exist.Methods
To investigate this, knowledge of the proteolytic properties of Der p 1 was used to perform in silico digestion of human dendritic cell surface proteins, using the prediction of protease specificity (PoPS) bioinformatics tool, in conjunction with cellular in vitro analysis and cleavage site determination.Results
Targets identified included DC‐SIGN and DC‐SIGNR, two C‐type lectins implicated mostly in pathogen trafficking. Treatment of positively expressing cells with Der p 1 led to loss of detectable surface DC‐SIGN and DC‐SIGNR. Digestion of purified soluble recombinant DC‐SIGN and DC‐SIGNR, followed by N‐terminal sequencing and MALDI mass spectrometry, indicated in each case one major cleavage site and several minor sites, the former correlating well with Der p 1 enzymology and the folded state of the substrate proteins. Loss of DC‐SIGN from the cell surface led to reduced binding of intracellular adhesion molecule‐3, an endogenous DC‐SIGN ligand expressed on naïve T cells which is thought to be involved in T‐helper type 1 cytokine signalling.Conclusion
These data provide evidence of lectin involvement in the initiation of the allergic response and the value of using genome‐wide in silico digestion tools.
The impact of liquid‐based oral cytology on the diagnosis of oral squamous dysplasia and carcinoma
Authors: Navone R. , Burlo P. , Pich A. , Pentenero M. , Broccoletti R. , Marsico A. , Gandolfo S. 
Published: January 2007

Objective:  Even though diagnostic oral exfoliative cytology is a useful, economical and practical tool in the diagnosis of oral dysplasia and carcinoma, it is not yet extensively used. The results of conventional exfoliative and liquid‐based diagnostic cytology in oral potentially malignant lesions (PML) are herein reported and compared with the histological diagnosis.Methods:  Either conventional (89) or liquid‐based (384) exfoliative cytology was used for the diagnosis of oral dysplasia/carcinoma in 473 subjects and the results were compared with scalpel biopsy histology. Cells were collected using a Cytobrush device for conventional smears and with a dermatological curette for the liquid‐based cytology. The ‘curette technique’ also allowed for the collection of ‘accidental’ tissue fragments, utilized as microbiopsies.Results:  Histological diagnosis was squamous carcinoma in 96 of 473 cases, high‐grade dysplasia (oral intraepithelial neoplasia two to three) in 24 and other lesions in 353 cases. The smears in the conventional cytology group were inadequate in 12.4%, with an 85.7% sensitivity and a 95.9% specificity. There were 8.8% of inadequate specimens in the liquid‐based cytology group; sensitivity was 95.1% and specificity was 99.0%.Conclusions:  Although conventional cytology is useful when diagnosing oral PML (better sensitivity and predictive positive value if compared with the cervical smear test with similar specificity) and can improve the accuracy of histological diagnosis, liquid‐based cytology gives better results, as it not only enhances both sensitivity and specificity, but also provides material for further investigation (AgNORs, DNA, microbiopsies, etc.).
Fine needle aspiration cytology of lung lesions: a clinicopathological and cytopathological review of 150 cases with emphasis on the relation between the number of passes and the incidence of pneumothorax
Authors: Halloush R. A. , Khasawneh F. A. , Saleh H. A. , Soubani A. O. , Piskorowski T. J. , Al‐Abbadi M. A. 
Published: January 2007

Objective:  The aim of this study was to review the lung fine needle aspirations (FNA) that were done in our hospital between January 1998 and April 2004. Interobserver agreement, sample adequacy and the relation between the number of passes and the occurrence of pneumothorax are presented.Study design:  One hundred fifty cases of lung FNA from the department of pathology files were identified and the available specimens and patient charts were reviewed. The interobserver agreement was calculated. The relation between the number of passes and the subsequent development of pneumothorax was tested using Mann–Whitney U‐test.Results:  The material of 132 patients (88%) out of 150 were retrieved and reviewed. There were 85 cases of non‐small cell lung cancer (NSCLC) (64.4%), nine cases of small cell lung cancer (6.8%), five cases of metastatic cancer (3.8%) and 33 cases were reported negative for cancer (25%). The NSCLC included 36 cases of adenocarcinoma (27.3%), 32 cases of squamous cell carcinoma (24.2%), and 17 cases of large cell undifferentiated carcinoma (12.9%). The interobserver agreement k was 0.93, (95% CI 0.87–0.98). The majority of cases (95.5%) were considered adequate for interpretation. The charts of 138 patients (92%) were reviewed for postprocedure radiologically confirmed pneumothorax. Sixteen patients (11.6%) developed pneumothorax only three of whom (2%) required a chest tube for treatment. The number of passes was identified in 118 patients (85.5%). The number of passes did not have a statistically significant association with the development of a pneumothorax (P = 0.747).Conclusion:  Fine needle aspirations to diagnose lung lesions is a safe procedure with a low incidence of pneumothorax. Its findings are reproducible with high interobserver agreement. Immediate adequacy evaluation and triage by a pathologist guarantees adequate sample in most instances. The number of passes was not associated with an increased incidence of pneumothorax.
Local thermal injury elicits immediate dynamic behavioural responses by corneal Langerhans cells
Authors: Ward Brant R. , Jester James V. , Nishibu Akiko , Vishwanath Mridula , Shalhevet David , Kumamoto Tadashi , Petroll W. Matthew , Cavanagh H. Dwight , Takashima Akira 
Published: January 2007

SummaryLangerhans cells (LCs) represent a special subset of immature dendritic cells (DCs) that reside in epithelial tissues at the environmental interfaces. Although dynamic interactions of mature DCs with T cells have been visualized in lymph nodes, the cellular behaviours linked with the surveillance of tissues for pathogenic signals, an important function of immature DCs, remain unknown. To visualize LCs in situ, bone marrow cells from C57BL/6 mice expressing the enhanced green fluorescent protein (EGFP) transgene were transplanted into syngeneic wild‐type recipients. Motile activities of EGFP+ corneal LCs in intact organ cultures were then recorded by time lapse two‐photon microscopy. At baseline, corneal LCs exhibited a unique motion, termed dendrite surveillance extension and retraction cycling habitude (dSEARCH), characterized by rhythmic extension and retraction of their dendritic processes through intercellular spaces between epithelial cells. Upon pinpoint injury produced by infrared laser, LCs showed augmented dSEARCH and amoeba‐like lateral movement. Interleukin (IL)‐1 receptor antagonist completely abrogated both injury‐associated changes, suggesting roles for IL‐1. In the absence of injury, exogenous IL‐1 caused a transient increase in dSEARCH without provoking lateral migration, whereas tumour necrosis factor‐α induced both changes. Our results demonstrate rapid cytokine‐mediated behavioural responses by LCs to local tissue injury, providing new insights into the biology of LCs.
CXCR3‐mediated T‐cell chemotaxis involves ZAP‐70 and is regulated by signalling through the T‐cell receptor
Authors: Dar Wasim A. , Knechtle Stuart J. 
Published: January 2007

SummaryThe chemokine receptor CXCR3 is critical for the function of activated T cells. We studied the molecular mechanisms of CXCR3 signalling. The addition of CXCR3 ligands to normal human T cells expressing CXCR3 led to the tyrosine phosphorylation of multiple proteins. Addition of the same ligands to Jurkat T cells engineered to express CXCR3 induced tyrosine phosphorylation of proteins with molecular weights similar to those in normal cells. Immunoblotting with phosphotyrosine‐specific antibodies identified Zeta‐associated protein of 70 000 molecular weight (ZAP‐70), linker for the activation of T cells (LAT), and phospholipase‐C‐γ1 (PLCγ1) to be among the proteins that become phosphorylated upon CXCR3 activation. ZAP‐70 was phosphorylated on tyrosine 319, LAT on tyrosines 171 and 191, and PLCγ1 on tyrosine 783. The ZAP‐70 inhibitor piceatannol reduced CXCR3‐mediated tyrosine phosphorylation of ZAP‐70, LAT, PLCγ1 and mitogen‐activated protein kinase Erk and it reduced CXCL10‐mediated chemotaxis of both CXCR3‐transfected Jurkat T cells and normal T cells expressing CXCR3. These results are consistent with the involvement of ZAP‐70 in CXCR3‐mediated protein tyrosine phosphorylation and CXCR3‐induced T‐cell chemotaxis. Studies with the Lck‐deficient Jurkat T‐cell line, JCAM1.6, demonstrated that phosphorylation of ZAP‐70 after CXCR3 activation is a Lck‐dependent process. Finally, stimulating CXCR3‐expressing Jurkat T cells and normal T cells expressing CXCR3 through the T‐cell receptor attenuated CXCR3‐induced tyrosine phosphorylation and CXCR3‐mediated T‐cell migration, indicating the occurrence of cross‐talk between T‐cell receptor and CXCR3‐signalling pathways. These results shed light on the mechanisms of CXCR3 signalling. Such information could be useful when designing therapeutic strategies to regulate T‐cell function.
Murine pregnancy leads to reduced proliferation of maternal thymocytes and decreased thymic emigration
Authors: Zoller Allison L. , Schnell Frederick J. , Kersh Gilbert J. 
Published: January 2007

SummaryDuring mammalian pregnancy the maternal thymus undergoes significant involution, and then recovers in size after birth. The mechanism behind this involution is not known, but it has been suggested that elevated levels of hormones during pregnancy induce the involution. We have recently shown that injection of 17β‐oestradiol into mice causes loss of early thymocyte precursors and inhibits proliferation of developing thymocytes. This suggests that elevated oestrogen in pregnancy may contribute to thymic involution. We have investigated this idea by examining the fate of thymocytes during mouse pregnancy in much greater detail than has been previously reported. Looking over a broad time–course, we find that pregnancy does not affect thymocyte precursor populations in the bone marrow, but induces a profound loss of early thymic progenitors in the thymus as early as day 12·5 of pregnancy. This loss is accompanied by decreased thymocyte proliferation, which returns to normal 2–4 days postpartum. No enhancement of apoptosis is detectable at any stage of pregnancy. We also find that there is a reduction in recent thymic emigrants after oestrogen treatment and at day 17·5 of pregnancy, suggesting that thymic involution during pregnancy influences the peripheral T‐cell repertoire. The similarities between oestrogen‐mediated involution and pregnancy‐mediated involution suggest that oestrogen is a significant contributor to loss of thymocyte cellularity during pregnancy, and probably functions primarily by reducing thymocyte proliferation.
Social parasitism by workers in queenless and queenrightApis ceranacolonies
Authors: NANORK P. , CHAPMAN N. C. , WONGSIRI S. , LIM J. , GLOAG R. S. , OLDROYD B. P. 
Published: January 2007

AbstractWe examined worker reproduction in queenless and queenrightApis ceranacolonies to determine if they are parasitized by workers from other nests. The results demonstrate that 2–6% of workers in queenright colonies are from another nest (non‐natal), but these workers are not statistically more likely to have activated ovaries than natal workers, and are therefore unlikely to be active parasites. However, in queenless colonies we found a significant difference between the proportion of non‐natal (72.7%) and natal (36.3%) workers with activated ovaries. Non‐natal workers also had significantly higher reproductive success than natal workers: 1.8% of workers were non‐natal, but these laid 5.2% of the eggs and produced 5.5% of the pupae. UnlikeA. florea, the proportion of non‐natal workers does not increase in queenless nests.