Search

In this study, a generalization of the Pell sequence called bi-periodic Pell sequence is carried out to matrix theory. Therefore, we call this matrix sequence the bi-periodic Pell matrix sequence whose entries are bi-periodic Pell numbers. Then the generating function, Binet formula and some basic properties and sum formulas are examined. [ABSTRACT FROM AUTHOR]

In this paper, the bi-periodic Jacobsthal Lucas sequence will be carried to matrix algebra. The terms of the bi-periodic Jacobsthal Lucas matrix sequence are the bi-periodic Jacobsthal Lucas numbers. By studying the properties of this matrix sequence, the well-known Simpson's formula, generating function as well as the Binet formula are investigated. Some new properties and two summation formulas for this new generalized matrix sequence are also obtained. [ABSTRACT FROM AUTHOR]

Objective: To compare the features of sarcoidosis in children to those of adults. In spite of the fact that sarcoidosis is a disease frequently seen in adults of 30-40 years, pediatric cases have rarely been reported.Methods: The authors evaluated 17 (3.3%, 12 females, 5 males) of the 516 patients of sarcoidosis, aged 16 yr and diagnosed within a 36-year period.Results: When the features of sarcoidosis subjects diagnosed during the childhood period were compared to those of subjects >16 years of age, it was seen that patients with advanced stage of the disease were more in the first group (41.2% vs 18%, p=0.02). In addition, children had more frequent extrapulmonary (64.7% vs 40.3%) and lacrimal gland involvement (p values, respectively, 0.044 and 0.003).Conclusion: When clinical data are relevant, sarcoidosis should be borne in mind. A child with sarcoidosis has more frequent pulmonary parenchymal and extrapulmonary involvement than in adults. [ABSTRACT FROM AUTHOR]

Nowadays, Endoscopic transsphenoidal approach is accepted as the standard method for pituitary adenomas. Endoscope presents two-dimensional panoramic view of surgical field. The orientation of the surgical field becomes easier by the effective use of endoscope in short time and finding anatomic landmarks. Anatomic landmarks are the most important anatomic formations that surgeon has to find to form safe surgical field. Endoscopic Transsphenoidal Pituitary Surgery is carried out in four stages including preoperative preparation, nasal stage, sphenoidal stage and sellar stage. Superior-middle-inferior nasal conchas and sphenoid ostium are landmarks of nasal stage. By going forward through the inferior line of Concha Nasalis, concha nasalis media is leaned to lateral and by doing this concha nasalis superior becomes visible. Concha nasalis superior is approximately 1,5 cm above choanae and ostium sphenoidale with 1-2 mm diameter is just at the bottom of concha nasalis superior. Sphenovomerine suture is used for passing from nasal stage to sphenoidal stage. When sphenovomerine suture is removed, sellae base becomes clearly visible. Then, the sellae base becomes a surgical field with carotid prominence at the laterals and field from planum sphenoidale to clivus. Tumor is removed by preserving neurovascular structures. After the tumor is removed, it is checked whether there is CSF leak or not. If there is no leak, sellar reconstruction is unnecessary. If dura mater is preserved, it is re-placed and surgical field is covered with surgicel-spongostan. Preserved part of sinus mucosa is laid on surgical field and then the operation is finished. [ABSTRACT FROM AUTHOR]

The first transsphenoidal surgical approach to pituitary adenomas has been performed by Herman Schloffer with superiolateral nasoethmoidal approach in Austria Innsburg on March 16,1907. Hirsch has applied endonasal transseptal transsphenoidal approach in 1910. In 1960s, by the usage of microscope in operations, endoscopic endonasal transsphenoidal approach has been being used for pituitary adenomas. The first complete endoscopic approach to sella turcica has been performed in France by Jankowski and his friends to three patients in year 1992. In 1997 at Pittsburg University, neurosurgery expert Jho and otolaryngologist Carrau have performed complete pituitary adenoma excision surgery with their 50 case series. Till now, Enrico de Divitiis and Paolo Cappabianca (Napoli), Giorgio Frank (Bologna) from Italy, Amin Kassam from USA and Mustafa Berker from Turkey have contributed to the usage of complete endoscopic techniques for both glandula pituitary surgery and pathologies related with skull base. In the following years, recognition of endoscope by brain surgeons, approach to sellar and parasellar region gained a new perspective. Nowadays, endoscopic transsphenoidal approach has taken place of microscopic surgery for brain surgeons and has become standard approach at many clinical centers. [ABSTRACT FROM AUTHOR]

Definiteness has been argued to be difficult for language learners to acquire because the correct usage of definiteness requires the integration of external interfaces that involve linguistic and non-linguistic information. Previous offline studies with heritage speakers have constantly reported difficulties in the use of pragmatically appropriate definite forms. The current study aims to investigate the processing of definiteness in Turkish heritage speakers via a self-paced reading experiment and to compare heritage speakers' reading times and end-of-sentence acceptance percentage to monolingually-raised Turkish speakers. The results of the experiment indicate significant differences between the heritage and monolingually-raised Turkish speakers only in the end-of-sentence acceptance percentage data but not in the reading time data. This difference between the two groups suggests that Turkish heritage speakers perform differently from the monolingually-raised Turkish speakers only in indefinite-specific sentences when they have to use their metalinguistic knowledge. These results show that heritage speakers experience vulnerability/difficulty when they have to integrate external interfaces in indefinite-specific sentences but not in definite-specific sentences., Competing Interests: The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Uygun.)

Previous studies have reported that null subject is not completely lost in heritage speakers, but there is an increase in the production and acceptance of overt subjects. Turkish is a pro-drop language and as a typical feature of pro-drop languages, it requires obligatory verb agreement marking for sentences with null subjects. However, Turkish subject-verb agreement marking is an example of optional agreement in which the 3rd person plural subject has optionality and can be used with singular verb forms under certain conditions. The current study investigates the reading times (RTs) of plural-marked and unmarked verbs in sentences with overt and null subjects during real time sentence processing in comparison to non-heritage speakers of Turkish via a self-paced reading experiment. Significant differences were observed between the heritage and non-heritage speakers of Turkish indicating both quantitative and qualitative real-time processing differences between the two groups. These differences suggest that Turkish heritage speakers need more time to integrate the information in real time processing., Competing Interests: The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Uygun.)

Synergid cells in the micropylar end of the female gametophyte are required for critical cell-cell signaling interactions between the pollen tube and the ovule that precede double fertilization and seed formation in flowering plants. LORELEI (LRE) encodes a putative GPI-anchored protein that is expressed primarily in the synergid cells, and together with FERONIA, a receptor-like kinase, it controls pollen tube reception by the receptive synergid cell. Still, how LRE expression is controlled in synergid cells remains poorly characterized. We identified candidate cis-regulatory elements enriched in LRE and other synergid cell-expressed genes. One of the candidate motifs ('TAATATCT') in the LRE promoter was an uncharacterized variant of the Evening Element motif that we named as the Short Evening Element-like (SEEL) motif. Deletion or point mutations in the SEEL motif of the LRE promoter resulted in decreased reporter expression in synergid cells, demonstrating that the SEEL motif is important for expression of LRE in synergid cells. Additionally, we found that LRE expression is decreased in the loss of function mutants of REVEILLE (RVE) transcription factors, which are clock genes known to bind the SEEL and other closely related motifs. We propose that RVE transcription factors regulate LRE expression in synergid cells by binding to the SEEL motif in the LRE promoter. Identification of cis-regulatory elements and transcription factors involved in the expression of LRE will serve as a foundation to characterize the gene regulatory networks in synergid cells., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Plant metabolites from diverse pathways are important for plant survival, human nutrition and medicine. The pathway memberships of most plant enzyme genes are unknown. While co-expression is useful for assigning genes to pathways, expression correlation may exist only under specific spatiotemporal and conditional contexts. Utilising > 600 tomato (Solanum lycopersicum) expression data combinations, three strategies for predicting memberships in 85 pathways were explored. Optimal predictions for different pathways require distinct data combinations indicative of pathway functions. Naive prediction (i.e. identifying pathways with the most similarly expressed genes) is error prone. In 52 pathways, unsupervised learning performed better than supervised approaches, possibly due to limited training data availability. Using gene-to-pathway expression similarities led to prediction models that outperformed those based simply on expression levels. Using 36 experimental validated genes, the pathway-best model prediction accuracy is 58.3%, significantly better compared with that for predicting annotated genes without experimental evidence (37.0%) or random guess (1.2%), demonstrating the importance of data quality. Our study highlights the need to extensively explore expression-based features and prediction strategies to maximise the accuracy of metabolic pathway membership assignment. The prediction framework outlined here can be applied to other species and serves as a baseline model for future comparisons., (© 2021 The Author(s) New Phytologist © 2021 New Phytologist Foundation.)

Background: In this phase II clinical trial, we evaluated the efficacy of the nonanthracycline combination of carboplatin and nab-paclitaxel in early stage triple-negative breast cancer (TNBC)., Patients and Methods: Patients with newly diagnosed stage II-III TNBC (n = 69) were treated with neoadjuvant carboplatin (area under the curve 6) every 28 days for four cycles plus nab-paclitaxel (100 mg/m 2 ) weekly for 16 weeks. Pathological complete response (pCR) and residual cancer burden (RCB) were analyzed with germline mutation status, tumor-infiltrating lymphocytes (TILs), TNBC molecular subtype, and GeparSixto immune signature (GSIS)., Results: Sixty-seven patients were evaluable for safety and response. Fifty-three (79%) patients experienced grade 3/4 adverse events, including grade 3 anemia (43%), neutropenia (39%), leukopenia (15%), thrombocytopenia (12%), fatigue (7%), peripheral neuropathy (7%), neutropenia (16%), and leukopenia (1%). Twenty-four patients (35%) had at least one dose delay, and 50 patients (72%) required dose reduction. Sixty-three (94%) patients completed scheduled treatment. The responses were as follows: 32 of 67 patients (48%) had pCR (RCB 0), 10 of 67 (15%) had RCB I, 19 of 67 (28%) had RCB II, 5 of 67 (7%) had RCB III, and 1 of 67 (2%) progressed and had no surgery. Univariate analysis showed that immune-hot GSIS and DNA repair defect (DRD) were associated with higher pCR with odds ratios of 4.62 (p = .005) and 4.76 (p = .03), respectively, and with RCB 0/I versus RCB II/III with odds ratio 4.80 (p = .01). Immune-hot GSIS was highly correlated with DRD status (p = .03), TIL level (p < .001), and TNBC molecular subtype (p < .001). After adjusting for age, race, stage, and grade, GSIS remained associated with higher pCR and RCB class 0/I versus II/III with odds ratios 7.19 (95% confidence interval [CI], 2.01-25.68; p = .002) and 8.95 (95% CI, 2.09-38.23; p = .003), respectively., Conclusion: The combination of carboplatin and nab-paclitaxel for early stage high-risk TNBC showed manageable toxicity and encouraging antitumor activity. Immune-hot GSIS is associated with higher pCR rate and RCB class 0/1. This study provides an additional rationale for using nonanthracycline platinum-based therapy for future neoadjuvant trials in early stage TNBCs. Clinical trial identification number: NCT01525966 IMPLICATIONS FOR PRACTICE: Platinum is an important neoadjuvant chemotherapy agent for treatment of early stage triple-negative breast cancer (TNBC). In this study, carboplatin and nab-paclitaxel were well tolerated and highly effective in TNBC, resulting in pathological complete response of 48%. In univariate and multivariate analyses adjusting for age, race, tumor stage and grade, "immune-hot" GeparSixto immune signature (GSIS) and DNA repair defect (DRD) were associated with higher pathological complete response (pCR) and residual cancer burden class 0/1. The association of immune-hot GSIS with higher pCR holds promise for de-escalating neoadjuvant chemotherapy for patients with early stage TNBC. Although GSIS is not routinely used in clinic, further development of this immune signature into a clinically applicable assay is indicated., (© 2020 AlphaMed Press.)

Lack of effective medical treatment in infantile colic (IC) causes desperate mothers to apply for complementary and alternative medicine (CAM) treatments. Due to the possibility of benefits, the risks that may be incurred by these methods are often ignored by the parents. Therefore, information on the use of CAM methods in IC is needed. The aim of this study is to reveal the CAM experiences of mothers in IC treatment and the demographic characteristics that affect them. Mothers whose children were diagnosed as IC by a physician in the past were included in the study. The sociodemographic characteristics of the mothers, IC-diagnosed baby characteristics and CAM experiences were investigated face to face with a structured questionnaire. Sixty-six of 96 mothers who participated in the study used the CAM method. There was a statistically significant difference between the use of CAM and the education level of mothers ( p < 0.05). We determined that 74% of mothers informed their doctors before starting treatments, and 82% do not believe if the CAM method could cause any harm that they would not notice by observing. The results showed that CAM methods are commonly used in IC treatment. According to these findings, mothers who use these methods believe that they are always harmless and have no side effects. For this reason, physicians should be careful about the adverse effects that may occur due to the CAM methods, which are widely used., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © Sudanese Association of Pediatricians.)

Multicellular organisms have diverse cell types with distinct roles in development and responses to the environment. At the transcriptional level, the differences in the environmental response between cell types are due to differences in regulatory programs. In plants, although cell-type environmental responses have been examined, it is unclear how these responses are regulated. Here, we identify a set of putative cis-regulatory elements (pCREs) enriched in the promoters of genes responsive to high-salinity stress in six Arabidopsis ( Arabidopsis thaliana ) root cell types. We then use these pCREs to establish cis-regulatory codes (i.e. models predicting whether a gene is responsive to high salinity for each cell type with machine learning). These pCRE-based models outperform models using in vitro binding data of 758 Arabidopsis transcription factors. Surprisingly, organ pCREs identified based on the whole-root high-salinity response can predict cell-type responses as well as pCREs derived from cell-type data, because organ and cell-type pCREs predict complementary subsets of high-salinity response genes. Our findings not only advance our understanding of the regulatory mechanisms of the plant spatial transcriptional response through cis-regulatory codes but also suggest broad applicability of the approach to any species, particularly those with little or no trans-regulatory data., (© 2019 American Society of Plant Biologists. All Rights Reserved.)

The evolution of transcriptional regulatory mechanisms is central to how stress response and tolerance differ between species. However, it remains largely unknown how divergence in cis -regulatory sites and, subsequently, transcription factor (TF) binding specificity contribute to stress-responsive expression divergence, particularly between wild and domesticated species. By profiling wound-responsive gene transcriptomes in wild Solanum pennellii and domesticated S. lycopersicum , we found extensive wound response divergence and identified 493 S. lycopersicum and 278 S. pennellii putative cis -regulatory elements (pCREs) that were predictive of wound-responsive gene expression. Only 24-52% of these wound response pCREs (depending on wound response patterns) were consistently enriched in the putative promoter regions of wound-responsive genes across species. In addition, between these two species, their differences in pCRE site sequences were significantly and positively correlated with differences in wound-responsive gene expression. Furthermore, ∼11-39% of pCREs were specific to only one of the species and likely bound by TFs from different families. These findings indicate substantial regulatory divergence in these two plant species that diverged ∼3-7 million years ago. Our study provides insights into the mechanistic basis of how the transcriptional response to wounding is regulated and, importantly, the contribution of cis -regulatory components to variation in wound-responsive gene expression between a wild and a domesticated plant species., (© 2018 American Society of Plant Biologists. All rights reserved.)

Facing adverse conditions such as nitrogen (N) deprivation, microalgae enter cellular quiescence, a reversible cell cycle arrest with drastic changes in metabolism allowing cells to remain viable. Recovering from N deprivation and quiescence is an active and orderly process as we are showing here for Chlamydomonas reinhardtii We conducted comparative transcriptomics on this alga to discern processes relevant to quiescence in the context of N deprivation and recovery following refeeding. A mutant with slow recovery from N deprivation, compromised hydrolysis of triacylglycerols7 ( cht7 ), was included to better define the regulatory processes governing the respective transitions. We identified an ordered set of biological processes with expression patterns that showed sequential reversal following N resupply and uncovered acclimation responses specific to the recovery phase. Biochemical assays and microscopy validated selected inferences made based on the transcriptional analyses. These comprise (1) the restoration of N source preference and cellular bioenergetics during the early stage of recovery; (2) flagellum-based motility in the mid to late stage of recovery; and (3) recovery phase-specific gene groups cooperating in the rapid replenishment of chloroplast proteins. In the cht7 mutant, a large number of programmed responses failed to readjust in a timely manner. Finally, evidence is provided for the involvement of the cAMP-protein kinase A pathway in gating the recovery. We conclude that the recovery from N deprivation represents not simply a reversal of processes directly following N deprivation, but a distinct cellular state., (© 2018 American Society of Plant Biologists. All Rights Reserved.)

Plants are exposed to a variety of environmental conditions, and their ability to respond to environmental variation depends on the proper regulation of gene expression in an organ-, tissue-, and cell type-specific manner. Although our knowledge of how stress responses are regulated is accumulating, a genome-wide model of how plant transcription factors (TFs) and cis-regulatory elements control spatially specific stress response has yet to emerge. Using Arabidopsis ( Arabidopsis thaliana ) as a model, we identified a set of 1,894 putative cis-regulatory elements (pCREs) that are associated with high-salinity (salt) up-regulated genes in the root or the shoot. We used these pCREs to develop computational models that can better predict salt up-regulated genes in the root and shoot compared with models based on known TF binding motifs. In addition, we incorporated TF binding sites identified via large-scale in vitro assays, chromatin accessibility, evolutionary conservation, and pCRE combinatorial relationships in machine learning models and found that only consideration of pCRE combinations led to better performance in salt up-regulation prediction in the root and shoot. Our results suggest that the plant organ transcriptional response to high salinity is regulated by a core set of pCREs and provide a genome-wide view of the cis-regulatory code of plant spatial transcriptional responses to environmental stress., (© 2017 American Society of Plant Biologists. All Rights Reserved.)

Plant transcription factors (TFs) that interact with specific sequences via DNA-binding domains are crucial for regulating transcriptional initiation and are fundamental to plant development and environmental response. In addition, expansion of TF families has allowed functional divergence of duplicate copies, which has contributed to novel, and in some cases adaptive, traits in plants. Thus, TFs are central to the generation of the diverse plant species that we see today. Major plant agronomic traits, including those relevant to domestication, have also frequently arisen through changes in TF coding sequence or expression patterns. Here our goal is to provide an overview of plant TF evolution by first comparing the diversity of DNA-binding domains and the sizes of these domain families in plants and other eukaryotes. Because TFs are among the most highly expanded gene families in plants, the birth and death process of TFs as well as the mechanisms contributing to their retention are discussed. We also provide recent examples of how TFs have contributed to novel traits that are important in plant evolution and in agriculture.This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Gene co-expression has been widely used to hypothesize gene function through guilt-by association. However, it is not clear to what degree co-expression is informative, whether it can be applied to genes involved in different biological processes, and how the type of dataset impacts inferences about gene functions. Here our goal is to assess the utility and limitations of using co-expression as a criterion to recover functional associations between genes. By determining the percentage of gene pairs in a metabolic pathway with significant expression correlation, we found that many genes in the same pathway do not have similar transcript profiles and the choice of dataset, annotation quality, gene function, expression similarity measure, and clustering approach significantly impacts the ability to recover functional associations between genes using Arabidopsis thaliana as an example. Some datasets are more informative in capturing coordinated expression profiles and larger data sets are not always better. In addition, to recover the maximum number of known pathways and identify candidate genes with similar functions, it is important to explore rather exhaustively multiple dataset combinations, similarity measures, clustering algorithms and parameters. Finally, we validated the biological relevance of co-expression cluster memberships with an independent phenomics dataset and found that genes that consistently cluster with leucine degradation genes tend to have similar leucine levels in mutants. This study provides a framework for obtaining gene functional associations by maximizing the information that can be obtained from gene expression datasets., Competing Interests: The authors have declared that no competing interests exist.

Purpose: Articulation of rostrum of sphenoid bone with alae of vomer forms a schindylesis type of joint. The circumference of this joint, called sphenovomerine suture (SVS), is very important in establishing a reliable surgical field in the endoscopic transsphenoidal pituitary surgery. Because of its vital role in endoscopic transsphenoidal pituitary surgery, this radio-anatomical study was designed to establish the morphological properties of SVS., Methods: In this study, the authors examined SVS in 235 patients (121 females and 114 males) on the computed tomography images of the paranasal sinus and made 4 measurements to describe SVS., Results: The mean distance between superior margin of the upper labial philtrum and top of SVS was 6.66 ± 0.43 cm for females and 7.44 ± 0.54 cm for males. The distance between the top of SVS and dorsum sellae was 3.08 ± 0.33 cm for females and 3.19 ± 0.32 cm for males, the alae of vomer angle in the upper surface was 74.22 ± 20.06° for females and 74.23 ± 19.68° for males. The distance between the most lateral points of 2 alae of vomer was 0.99 ± 0.17 and 1.01 ± 0.19 cm for females and males, respectively., Conclusions: For an easy and successful operation, removal of the SVS is very important as it will provide a better view of the sellar base and make the management of the surgical instruments easier in the wider safe surgical field thus created.

Jeune syndrome (Asphyxiating thoracic dysplasia) is a rare dystrophy of the skeleton, inherited as an autosomal recessive condition. Patients develop a narrowed thorax, rhizomelic dwarfism, and hepatic, renal, and pancreatic abnormalities. High rates of pulmonary hypoplasia and pulmonary hypertension have been reported. Some patients die in early stages of life due to respiratory failure. The case of a patient referred with a history of severe asphyxiating birth, who had been diagnosed with Jeune syndrome and later hypertrophic cardiomyopathy (HCM) upon echocardiographic examination is described in the present report. This rare disease is discussed with respect to the current literature, as the present is the first reported case to be accompanied by HCM.

The branched-chain amino acids (BCAAs) Leu, Ile, and Val are among nine essential amino acids that must be obtained from the diet of humans and other animals, and can be nutritionally limiting in plant foods. Despite genetic evidence of its importance in regulating seed amino acid levels, the full BCAA catabolic network is not completely understood in plants, and limited information is available regarding its regulation. In this study, transcript coexpression analyses revealed positive correlations among BCAA catabolism genes in stress, development, diurnal/circadian, and light data sets. A core subset of BCAA catabolism genes, including those encoding putative branched-chain ketoacid dehydrogenase subunits, is highly expressed during the night in plants on a diel cycle and in prolonged darkness. Mutants defective in these subunits accumulate higher levels of BCAAs in mature seeds, providing genetic evidence for their function in BCAA catabolism. In addition, prolonged dark treatment caused the mutants to undergo senescence early and overaccumulate leaf BCAAs. These results extend the previous evidence that BCAAs can be catabolized and serve as respiratory substrates at multiple steps. Moreover, comparison of amino acid profiles between mature seeds and dark-treated leaves revealed differences in amino acid accumulation when BCAA catabolism is perturbed. Together, these results demonstrate the consequences of blocking BCAA catabolism during both normal growth conditions and under energy-limited conditions., (© 2015 American Society of Plant Biologists. All Rights Reserved.)

Background: The aim of this study was to determine whether anterior rhinoscopy (AR), nasal endoscopy (NE) and paranasal sinus computed tomography (PNS CT) can predict other sinonasal obstructive pathologies in the setting of nasal septal deviation (NSD), and to evaluate the impact of preoperative PNS CT on the decision for a surgical procedure in patients with NSD., Methods: A total of 262 patients with NSD were evaluated using AR, NE, PNS CT, and the visual analogue scale (VAS) for nasal obstruction. The diagnostic values of AR, NE, and PNS CT for sinonasal obstructive pathologies, and the impact of preoperative PNS CT on the decision for a surgical procedure in patients with NSD were evaluated., Results: PNS CT showed concomitant nasal pathologies in the 62 of 262 patients (23.6%) with NSD. Positive predictive value (PPV) and negative predictive value (NPV) of NE for concomitant nasal pathologies were 0.75 and 0.069, respectively. The sensitivity of NE for sinonasal pathologies was significantly higher in the patients with mild NSD than in the patients with moderate-severe NSD. The decision for a surgical procedure was changed in 22 of 262 (8.3%) patients after a PNS CT., Conclusion: We recommend performing preoperative PNS CTs on patients in whom septoplasty is planned, if they have obstructive middle turbinate hypertrophy, if one is unable to evaluate the middle meatus and posterior nasal cavity because of an anteriorly severe deviation or a nasal polyp, and in patients with chronic sinusitis based on clinical and endoscopic findings., (© 2015 ARS-AAOA, LLC.)

Functional divergence between duplicate transcription factors (TFs) has been linked to critical events in the evolution of land plants and can result from changes in patterns of expression, binding site divergence, and/or interactions with other proteins. Although plant TFs tend to be retained post polyploidization, many are lost within tens to hundreds of million years. Thus, it can be hypothesized that some TFs in plant genomes are in the process of becoming pseudogenes. Here, we use a pair of salt tolerance-conferring transcription factors, DWARF AND DELAYED FLOWERING1 (DDF1) and DDF2, that duplicated through paleopolyploidy 50 to 65 million years ago, as examples to illustrate potential mechanisms leading to duplicate retention and loss. We found that the expression patterns of Arabidopsis thaliana (At)DDF1 and AtDDF2 have diverged in a highly asymmetric manner, and AtDDF2 has lost most inferred ancestral stress responses. Consistent with promoter disablement, the AtDDF2 promoter has fewer predicted cis-elements and a methylated repetitive element. Through comparisons of AtDDF1, AtDDF2, and their Arabidopsis lyrata orthologs, we identified significant differences in binding affinities and binding site preference. In particular, an AtDDF2-specific substitution within the DNA-binding domain significantly reduces binding affinity. Cross-species analyses indicate that both AtDDF1 and AtDDF2 are under selective constraint, but among A. thaliana accessions, AtDDF2 has a higher level of nonsynonymous nucleotide diversity compared with AtDDF1. This may be the result of selection in different environments or may point toward the possibility of ongoing functional decay despite retention for millions of years after gene duplication., (© 2015 American Society of Plant Biologists. All Rights Reserved.)

Background: Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based similarity because of the limited proportion of genes that are annotated to GO in most organisms., Results: We introduce a novel approach called NETSIM (network-based similarity measure) that incorporates information from gene co-function networks in addition to using the GO structure and annotations. Using metabolic reaction maps of yeast, Arabidopsis, and human, we demonstrate that NETSIM can improve the accuracy of GO term similarities. We also demonstrate that NETSIM works well even for genomes with sparser gene annotation data. We applied NETSIM on large Arabidopsis gene families such as cytochrome P450 monooxygenases to group the members functionally and show that this grouping could facilitate functional characterization of genes in these families., Conclusions: Using NETSIM as an example, we demonstrated that the performance of a semantic similarity measure could be significantly improved after incorporating genome-specific information. NETSIM incorporates both GO annotations and gene co-function network data as a priori knowledge in the model. Therefore, functional similarities of GO terms that are not explicitly encoded in GO but are relevant in a taxon-specific manner become measurable when GO annotations are limited. Supplementary information and software are available at http://www.msu.edu/~jinchen/NETSIM .

During routine anatomical dissection of the upper extremity of a 64-year-old cadaver for educational purposes, we observed variations in the brachial plexus on each side. On the right an anomaly of cord formation was present and on the left there was a communication between the musculocutaneous nerve (MCN) and median nerve (MN). On the right side the brachial plexus showed two trunks, superior (C5 and C6) and inferior (C7, C8, and T1); the middle trunk was absent. The superior trunk bifurcated into anterior and posterior divisions, the anterior division continued as the lateral cord forming the MCN. The posterior division gave off the subscapular branch. The inferior trunk trifurcated into radial, median, and ulnar nerves. The radial nerve gave off the axillary and thoracodorsal nerves. The ulnar nerve gave off the median cutaneous nerves of the arm and forearm. The median nerve received a small ascending branch from the MCN. On the right side, there was a communicating branch from the MCN to the MN in the lower third of the arm region. This communicating branch also gave rise to a muscular branch to the brachialis muscle and the lateral cutaneous nerve of forearm. No additional heads of the biceps brachii muscle were observed in either upper limb. Knowledge of the variations of the brachial plexus in humans can be valuable for operations of the shoulder joint and its repair for providing an effective block or treatment for anesthetists and also for explaining otherwise incomprehensible clinical signs for neurologists., (Georg Thieme Verlag KG Stuttgart · New York.)

A peripheral lymph node (PLN) 1 cm or greater was found in 79 of 546 sarcoidosis patients (14.5%) between 1972 and 2005. Seventy-two of the 79 sarcoidosis patients had a lymph node biopsy performed. Sixty-seven of these biopsy specimens were histologically diagnosed as sarcoidosis, whereas five patients had a reactive adenopathy. For patients with histological diagnosis of sarcoidosis, localizations of the biopsies were as follows: cervical (n=21), supraclavicular (n=20), inguinal (n=11), axillary (n=8), epitrochlear (n=5) and submandibular (n=2). At the time of biopsy, 12 patients had stage 0 disease, 37 patients had stage I disease, 14 patients had stage II disease and four patients had stage III disease. Skin involvement (16.4%) was the most frequently observed type of organ involvement in patients who had enlarged PLNs due to sarcoidosis. In the presence of an enlarged PLN in sarcoidosis, biopsy had a greater diagnostic value compared with other methods, as well as having a relatively low cost (approximately US$120) in Turkey. No procedure-related complications were observed. In conclusion, it is recommended that PLNs be thoroughly examined when sarcoidosis is suspected. If an enlarged PLN is found, biopsy should be routinely performed because it is an easy, convenient and practical method, with a low complication risk and a high sensitivity.

Principles and Methods: Upper respiratory tract (URT) involvement is rare in sarcoidosis. In this descriptive study, we retrospectively evaluated the clinical and demographic features of 12 (2.19%) patients with URT involvement out of the 546 sarcoidosis patients with follow-up visits at our center within the last 40-year period., Results: Out of the 546 patients, 12 (2.19%) had upper respiratory tract involvement, 5 (0.91%) had laryngeal involvement, 4 (0.73%) had sinonasal tract involvement, 2 (0.36) patients had salivary gland involvement, and 1 patient had tonsillary involvement. The number of stage 0 subjects among other sarcoidosis patients was significantly lower than that among those with URT involvement., Conclusions: URT involvement is rarely diagnosed in patients with systemic sarcoidosis. The most common site for URT involvement among the Turkish population is the larynx, followed by the sinonasal tract., Ebm Rating: C-4.

Background: Clinical manifestations and prognosis of sarcoidosis are heterogenous and the prevalence varies depending on the country, area and race evaluated. Also the organs involved and courses of the disease differ greatly between countries, areas, races and individuals., Aims: To investigate the sociodemographic characteristics, clinical presentation and symptoms and to determine the severity and prognosis of sarcoidosis in Turkey as a referral center., Methods: Between January and July 2003 we retrospectively evaluated the outcome of the patients with sarcoidosis whose first clinical visits were between 1965 and 2003 in the multidisciplinary referral setting RS at Cerrahpasa Medical Faculty of the University of Istanbul. Data collected about each patient included sociodemographic characteristics, clinical presentation, symptoms, date of diagnosis, date and age of onset, method and stage of disease at the date of diagnosis and at the date of last evaluation; the mortality and survival rate were calculated. One hundred and sixty six consecutive patients whose first clinical visits were between 1965 and 2003 in the multidisciplinary RS at Cerrahpasa Medical Faculty were enrolled. We contacted every patient in our cohort by telephone calls or home visits. All those contacted were called back to outpatient clinic for a formal evaluation between June and September 2003. A formal physical examination and thorax radiography were performed in patients who came to the hospital. Their radiological stage, signs, symptoms and associated extrapulmonary manifestations were recorded., Results: At the initial presentation, the mean age of diagnosis was 40.3 years. The 31-40 age group is the group with the highest number of patients. Coughing was the most frequent symptom and erythema nodosum was the most frequent sign in both sexes. Thirty eight percent of patients had extrathoracic involvement. The most frequent extrapulmonary site of involvement was skin. The mortality rate was 11.6% (10.8% in females and 13% in males). Comorbidity was 3% (5 females, 1 male). Females, youngs and patients without extrathoracic involvement had higher survival rates., Conclusion: Clinical characteristics, course and prognosis of sarcoidosis vary in different studies. The results may vary accordingly to ethnic, geographic, social and economic conditions.