bluuebunny/crossref_metadata_2025 huggingface dataset:
Philosophy of Science: How to Identify the Potential Research for the Day after Tomorrow?
Authors: Ventegodt Søren , Merrick Joav
Published: March 2005

We were asked to participate in a workshop to assist the European Commission on how to choose financial support for high-potential, basic research projects that can give new scientific breakthroughs and thus contribute significantly to the positive development of society, industry, and economy for the day after tomorrow. At this workshop, we analyzed the problem in some detail using experience from our own research on the global quality of life. We would suggest that the most promising projects have the following characteristics: (1) they are led by a brilliant researcher who considers his/her research to be “sweet science”, who wants to explain the anomalies of his/her field of science, and who lives in a nonmainstream scientific paradigm; (2) they are deeply engaged in the philosophical problems of their research field, they are searching eagerly for a new understanding and a new theory, giving new tools for measurement and creating change, and results are taken as feedback on all levels from tool to theory and philosophy; (3) they are focused on the key point(s), which is an essential feature of the universe that creates global change if intervened upon. At the NEST Pathfinder 2005 Topic Identification Workshop, Brussels 28 May 2004 entitled “Measuring the Impossible”, we advised the European Commission Research Directorate to allocate funds for projects focusing on the state of consciousness  how to understand it, how to map it, and how to develop it.
Magnesium, Aging, and the Elderly Patient
Authors: Davidovic Mladen , Trailov Dejan , Milosevic Dragoslav , Radosavljevic Branimir , Milanovic Pavle , Djurica Snezana , Loncar-Stevanovic Helena , Stevic Radmila
Published: March 2005

Magnesium, beyond any doubt, plays an important role in metabolism. Alterations of magnesium levels have an impact on many organs and systems, especially during aging. We had 156 participants aged 60–93 years (average 74.7 years) in our survey. Of them, 49 were men and 107 were women. Treatment with loop diuretics (Furosemid and Bumetanide) and magnesium levels was correlated, as well as the influence of magnesium levels on life span. Serum magnesium levels were measured in patients receiving diuretics and in the control group. Also, magnesium levels were measured in patients who passed away in the course of their disease and were compared with the control group. Magnesium levels in the diuretic group (100 patients) were 0.93 ± 0.094 mmol/l, while the average levels in the control group of 56 patients were 0.89 ± 0.075 mmol/l. In 29 patients who passed away, average magnesium levels were 0.92 ± 0.078 mmol/l, while in the control group (127 patients), magnesium levels were 0.93 ± 0.083 mmol/l. The differences were not statistically significant. There were no differences in serum magnesium of the elderly persons investigated regarding age group, gender, or type of diuretics. If methods of determining ionizing magnesium in serum or intracellular magnesium are not available, normal magnesium values in the serum are to be taken with a qualified acceptance.
Clinical Holistic Medicine: A Psychological Theory of Dependency to Improve Quality of Life
Authors: Ventegodt Søren , Morad Mohammed , Kandel Isack , Merrick Joav
Published: March 2005

In this paper, we suggest a psychological theory of dependency as an escape from feeling existential suffering and a poor quality of life. The ways in which human beings escape hidden existential pains are multiple. The wide range of dependency states seems to be the most common escape strategy used. If the patient can be guided into the hidden existential pain to feel, understand, and integrate it, we believe that dependency can be cured. The problem is that the patient must be highly motivated, sufficiently resourceful, and supported to want such a treatment that is inherently painful. Often, the family and surrounding world is suffering more than the dependent person himself, because the pattern of behavior the patient is dependent on makes him or her rather insensitive and unable to feel. If the patient is motivated, resourceful, and trusts his physician, recovery from even a severe state of dependency is not out of reach, if the holistic medical tools are applied wisely. The patient must find hidden resources to take action, then in therapy confront and feel old emotional pain, understand the source and inner logic of it, and finally learn to let go of negative attitudes and beliefs. In this way, the person can be healed and released of the emotional suffering and no longer be a slave to the dependency pattern.
Evaluation of the Drug Treatment and Persistence of Onychomycosis
Authors: Campbell Andrew W. , Anyanwu Ebere C. , Morad Mohammed
Published: March 2005

Onychomycosis is a common nail disease responsible for approximately 50% of diseases of the nail. It occurs more in the elderly, though several cases have been reported among children. Several factors influence, such as climate, geography, and migration. The two dermatophytes most commonly implicated in onychomycosis are Trichophyton rubrum and T. mentagrophytes, accounting for more than 90% of onychomycoses. Nonetheless, several other toxigenic molds have been implicated. For convenience, onychomycosis is divided into four major clinical presentations: distal subungal, which is the most common form of the disease; proximal subungal, which is the most common form found in patients with human immunodeficiency virus infection; superficial; and total dystrophic onychomycosis. Epidemiology of onychomycosis in adults and children is evaluated and the most common clinical symptoms addressed. Although the risk factors are discussed, the multifactorial nature of onychomycosis makes this inexhaustible. The diagnosis and treatments are difficult and the choice of appropriate antifungal drugs complex and require the knowledge of the chemical structures of the metabolites of the molds that cause onychomycosis and their interaction with the antifungal drugs. This is true because most of the antifungal drugs are derived from mold/fungal metabolism. Treatment with griseofulvin and amphotericin is displaced by the use of newer drugs from azole compounds, pyrimidines, and allylamines derivatives. Amorolfine, itraconazole, and ciclopirox nail lacquer solution 8 have gained support globally, but the side effects, drug resistance, and persistence of the disease are still a serious concern to the patients, just as economics and quality of life. Hence, the search for safer and more efficacious drug treatments are continuing.
Seasonal Evaluation of Antigenic Bacterial Infections Among Working Class in the Inner City of Houston
Authors: Anyanwu Ebere C. , Morad Mohammed , Campbell Andrew W.
Published: March 2005

This paper evaluates the monthly, quarterly, and seasonal variation of antigenic bacterial infections among the working class in the inner city of Houston using the Wellcogen Rapid Test methods. One of the aims was to demonstrate how this method could be used effectively in screening patients at risk and preventing the spread of antigenic bacteria such asStreptococcus pneumoniae,Haemophilus influenzaeb,Streptococcus(Strep b), andNeisseria meningitidis(mainly group c and b). A total of 2,837 patients were screened for bacterial infections; 908 (32%) were male and 1,929 (68%) were female. The age range was between 2 and 70 years. Of the total group, 356 (12.5%) patients were positive; 203 (57%) were female while 153 (43%) were male (male/female ratio of 1:1.3). Medically underserved and immune suppressed populations are the most affected by these bacterial infections. Blacks are the most affected (48%) compared to Native Americans (1%), but children under 10 years of age have the highest incidence. This research showed, in addition, that the Wellcogen Rapid Tests are effective (356 cases identified) for a rapid screening of infectious bacteria. Explanation for these results was probably due to poor living conditions, poor hygiene, and viral immune suppression in adults and immature immune systems in neonates and children under 10 years of age.
A Case Follow-Up Report: Possible Health Benefits of Extra Virgin Olive Oil
Authors: Shahtahmasebi Said , Shahtahmasebi Shahnaz
Published: March 2005

In the course of a case study, a number of issues regarding the dynamics of blood cholesterol levels were identified. In this follow-up report, these issues are addressed. For example, issues of past behaviour and seasonality, intraindividual variation, and nonstationarity appear important over and above controllable variables such as diet and exercise. In this report, we conceptualise an alternative protective role for the dynamic blood cholesterol levels in a healthy population. Furthermore, regular consumption of extra virgin olive oil as produced in this case study may interact with the dynamics of cholesterol naturally. We recommend that future studies of this kind ought to include a time series of blood cholesterol based on daily measurements or intervals much shorter than the bimonthly measurements and to include measures of overall well being as covariates.
Effects of 2.45-GHz Electromagnetic Fields with a Wide Range of SARs on Micronucleus Formation in CHO-K1 Cells
Authors: Koyama S. , Isozumi Y. , Suzuki Y. , Taki M. , Miyakoshi J.
Published: March 2005

There has been considerable discussion about the influence of high-frequency electromagnetic fields (HFEMF) on the human body. In particular, HFEMF used for mobile phones may be of great concern for human health. In order to investigate the properties of HFEMF, we have examined the effects of 2.45-GHz EMF on micronucleus (MN) formation in Chinese hamster ovary (CHO)-K1 cells. MN formation is induced by chromosomal breakage or inhibition of spindles during cell division and leads to cell damage. We also examined the influence of heat on MN formation, since HFEMF exposure causes a rise in temperature. CHO-K1 cells were exposed to HFEMF for 2 h at average specific absorption rates (SARs) of 5, 10, 20, 50, 100, and 200 W/kg, and the effects on these cells were compared with those in sham-exposed control cells. The cells were also treated with bleomycin alone as a positive control or with combined treatment of HFEMF exposure and bleomycin. Heat treatment was performed at temperatures of 37, 38, 39, 40, 41, and 42°C.The MN frequency in cells exposed to HFEMF at a SAR of lower than 50 W/kg did not differ from the sham-exposed controls, while those at SARs of 100 and 200 W/kg were significantly higher when compared with the sham-exposed controls. There was no apparent combined effect of HFEMF exposure and bleomycin treatment. On heat treatment at temperatures from 38–42°C, the MN frequency increased in a temperature-dependent manner. We also showed that an increase in SAR causes a rise in temperature and this may be connected to the increase in MN formation generated by exposure to HFEMF.
Influence of 50-Hz Electromagnetic Field on Anurian (Xenopus laevis) Metamorphosis
Authors: Grimaldi S. , Lisi A. , Reiti S. , Manni V. , Ledda M. , Giuliani L.
Published: March 2005

In this study, we show the effect of a 1-mT magnetic field AC at 50 Hz onXenopuslaevis tadpole populations. In the course of a 65-day exposure to the field, tadpole survival showed a small, but significant, decrease (p < 0.0004), together with a striking parallel 6-day shift in tadpole maturation frequency and a significant impairment of their metamorphosis. Particularly, metamorphosis was successful for 85% of individuals in the unirradiated tadpole population and for 45% of individuals in the irradiated tadpole population, respectively.
Clinical Holistic Medicine: Developing from Asthma, Allergy, and Eczema
Authors: Ventegodt Søren , Morad Mohammed , Merrick Joav
Published: March 2005

This paper shows how consciousness-based holistic medicine can be used in the case of asthma, allergy, and eczema. We have many fine drugs to relieve patients from the worst of these symptoms, where many children and adults suffer health problems related to hyper-reactivity of the immune system. Many symptoms remain throughout life because the drugs do not cure the allergy and allergy today is the sixth leading cause of chronic illness. The etiology of the immune disturbances is mostly unknown from a biomedical perspective. Consciousness-based holistic medicine could therefore be used to treat these diseases if the patient is willing to confront hidden existential pain, is motivated to work hard, and is dedicated to improve quality of life, quality of working life, and personal relationships. Improving quality of life is not always an easy job for the patient, but it can be done with coaching from the physician. An increased physical health is often observed after only a few sessions with a physician skilled in using holistic medical tools and able to coach the patient successfully through a few weeks of dedicated homework. Children with allergy and asthma can also be helped if their parents are able to do work on personal development, to improve the general quality of life in the family and their relationship with the child.
An Improved QSPR Modeling of Hydrocarbon Dipole Moments
Authors: Nesterov Igor V. , Toropov Andrey A. , Duchowicz Pablo R. , Castro Eduardo A.
Published: March 2005

Dipole moments of hydrocarbons are not an easy property to model with conventional 2D descriptors. A comparison of the performance of the most commonly used sets of topological descriptors is presented, each set containing descriptors derived from the regular and Detour distance matrix, Electrotopological State Indices, and the basic number of atoms of each type and bonds. Data were taken on a representative set of 35 hydrocarbon dipole moments previously reported and the classical multivariable regression analysis for establishing the models is employed.
Toward Molecular Level of the “Salmonella-Victim” Ecology, Genetics, and Evolution
Authors: Rumyantsev S.N.
Published: March 2005

Bacteria of theSalmonellagenus are polypathogenic agents that can affect both men and animals, causing devastating and fatal illness. Despite considerable immunological, epidemiological, and genetic efforts, and increased understanding of how theSalmonellainfection develops, many key questions concerningSalmonellainfection remain unanswered.Salmonellacan be carried as harmless commensals in some sectors of the population. In some individuals, however, the same microbes cause illness while others display immunity to primarySalmonellainfection. Nothing is known about the molecular base of theSalmonellapathogenicity. Even the ability ofSalmonellato destroy the victims cells has been the subject of century-long discussions. In this article, some key findings concerning ecology, molecular ecology, and cell level of theSalmonellainfection genetics are summarized and interpreted from the viewpoint of evolutionary theory with certitude that this approach can help to decipher the undiscovered secrets ofSalmonellainfections epidemiology and pathogenesis, as well as the clinical course and severity, and to select ways for fighting againstSalmonella.
Age-Related Molecular Polymorphism of the Heterodimeric Proteoglycan Bisdermican
Authors: Götte Martin , Sofeu Feugaing David D. , Kresse Hans
Published: March 2005

Bisdermican (PG760) is a large, heterodimeric, dermatan sulfate proteoglycan found in selected basement membranes, smooth muscle cell layers, and different extracellular matrices. Age-dependent and developmentally regulated alterations in glycosaminoglycan structure and quantity have been shown to be functionally relevant for a number of physiological and pathological processes. Bisdermican was purified from human skin fibroblast cultures of different age and confluency. Following β-elimination, glycosaminoglycan chains were analyzed by Sephacryl-S-300 chromatography. Glycosaminoglycan chains of Bisdermican from infantile fibroblasts had a molecular weight of 19 kDa, whereas the glycosaminoglycan chain of the large Bisdermican subunit purified from confluent fetal fibroblast secretions was slightly larger (Mr= 24 kDa). Bisdermican derived from subconfluent cultures of fetal fibroblasts displayed the largest glycosaminoglycan chains with a molecular weight of 31.5 kDa for the large subunit, and a molecular weight of 22 kDa for the small subunit. Thus, Bisdermican displays a molecular polymorphism that is related to its chronological age and proliferative state.
Clinical Holistic Medicine: Tools for a Medical Science Based on Consciousness
Authors: Ventegodt Søren , Morad Mohammed , Andersen Niels Jorgen , Merrick Joav
Published: March 2005

Biomedicine focuses on the biochemistry of the body, while consciousness-based medicine — holistic medicine — focuses on the individual's experiences and conscious whole (Greek: holos, whole). Biomedicine perceives diseases as mechanical errors at the micro level, while consciousness-based medicine perceives diseases as disturbances in attitudes, perceptions, and experiences at the macro level — in the organism as a whole. Thus, consciousness-based medicine is based on the whole individual, while biomedicine is based on its smallest parts, the molecules. These two completely different points of departure make the two forms of medicine very different; they represent two different mind sets and two different frames of reference or medical paradigms. This paper explains the basic tools of clinical holistic medicine based on the life mission theory and holistic process theory, with examples of holistic healing from the holistic medical clinic.
Solitary Contralateral Adrenal Metastases after Nephrectomy for Renal Cell Carcinoma
Authors: Antoniou Nikolaos , Karanastasis Demetrios
Published: March 2005

Two cases are reported of patients with a single metastasis in the contralateral adrenal, one and nine years respectively after nephrectomy for localized cancer in the opposite kidney. These types of metastases are usually asymptomatic they do not appear with signs of adrenal insufficiency, they are detected incidentally and the diagnosis is confirmed mainly with CT scan, which comprises the method of choice for the detection of such types of metastases. Many adrenal metastases probably have been overlooked in the past when advanced imaging techniques were not available. Both patients underwent adrenalectomy and replacement therapy with corticosteroids. Approximately 50% of all patients with renal cell carcinoma either present with metastases at diagnosis or will have metastatic disease after nephrectomy11. In order of decreasing frequency, the most common metastatic sites are the lungs, lymph nodes, liver, bone, contralateral kidney and ipsilateral adrenal glands. Adrenal involvement has been reported in 7 to 19% of autopsystudies.1,3Solitary metachronous metastatic involvement of the contralateral adrenal from renal cell carcinoma is rarely diagnosed during life and only 4 cases have been reported.4,5Recent advances in imaging techniques have allowed the diagnosis of adrenal involvement by renal cancer. Two cases of contralateral adrenal metastasis are reported 1 and 9 years after radical nephrectomy for localized renal cell carcinoma. Both patients underwent adrenalectomy and steroid replacement therapy.
Clinical Remission of Chronic Refractory Pelvic Symptoms in Three Men
Authors: Hennenfent Bradley R. , Feliciano Antonio Espinosa
Published: March 2005

We report on three American men with chronic refractory pelvic pain, urinary symptoms, and sexual dysfunction who traveled to the Philippines for treatment. In the Manila Genitourinary Clinic, the patients were treated with microbial diagnosis, antimicrobial therapy, and 19, 27, and 21 prostatic massages respectively. All three patients underwent resolution of symptoms.
Superselective Embolization of Arterial Bleeding as a Late Complication 3 Months After Nephron Sparing Surgery for Renal Cell Carcinoma
Authors: Thomas J. , Perabo F.G.E. , Bachmann R. , Steiner G. , Schild H. , Müller S.C.
Published: March 2005

To our knowledge, this is the first case of an arterial bleeding as a late complication 3 months after nephron sparing surgery of renal cell cancer, presumably originating from an arteriocalyceal fistula. Superselective embolization of the feeding arterial branch was chosen for treatment of the hemorrhage and proved successful. The high efficacy of superselective embolization as a minimally invasive procedure in this and other cases of bleeding Vessels should be the preferred method instead of open surgery.
Complete Ureteral Avulsion
Authors: Gupta V. , Sadasukhi T. C. , Sharma K. K. , Yadav R. G. , Mathur R. , Tomar V. , Yadav S. S. , Priyadarshi S. , Gupta P.
Published: March 2005

Complete avulsion of the ureter is one of the most serious complications of ureteroscopy. It requires open or laparoscopic intervention for repair. This case report emphasizes its management and presents recommendations for prevention in current urological practice.
Clinical Holistic Medicine: Chronic Pain in the Locomotor System
Authors: Ventegodt Søren , Merrick Joav
Published: March 2005

Most pains from the locomotor system arise due to involuntary, chronic tensions in the muscles or other tissues. When the patient is motivated, the pain is easily cured in most of the cases by using the tools of consciousness-based medicine, primarily therapeutic touch, conversation, and coaching the patient in a positive philosophy of life. The pains are often caused by “blockages” that may cause problems other than just pain. Often it turns out that the blocked areas develop actual physical damage over time: a slipped disk in the back, articular degeneration, or osteoarthritis when the cartilage is affected, can often be explained in this way. Apparently, the exact areas where the blockage is situated cause cellular problems, disrupting cellular order. The holistic process theory of healing and the related quality of life theories state that return to the natural state of being is possible, whenever the person gets the resources needed for existential healing. The resources needed are “holding” in the dimensions of awareness, respect, care, acknowledgment, and acceptance with support and processing in the dimensions of feeling, understanding, and letting go of negative attitudes and beliefs. The preconditions for holistic healing are trust and the intention for the healing to take place. Case stories of holistic treatment of patients with chronic back pain, low back pain, muscle problems, knee pain, and symptoms of rheumatoid arthritis are discussed with exercises relevant for patients with these conditions in the holistic clinic.
Metastatic Renal Cell Carcinoma versus Pancreatic Neuroendocrine Tumor in von Hippel-Lindau Disease: Treatment with Interleukin-2
Authors: Williams Christopher , Walther McClellan
Published: March 2005

Differentiating between clear cell neuroendocrine tumor (NET) of the pancreas and renal cell carcinoma (RCC) metastatic to the pancreas can be challenging in patients with von Hippel-Lindau disease (VHL). The clear cell features of both NET and RCC in VHL patients may lead to misdiagnosis, inaccurate staging, and alternative treatment. We present a patient in which this occurred. As clear cell NETs closely resembling metastatic RCC are distinctive neoplasms of VHL and metastatic RCC to the pancreas in the VHL population is rare, careful pathologic examination should be performed prior to subjecting patients to definitive surgical or medical therapies.
Applied K Fertilizer Use Efficiency in Pineapples Grown on a Tropical Peat Soil Under Residues Removal
Authors: Ahmed Osumanu H. , Ahmad Husni M. H. , Musa Hanafi M. , Rahim Anuar A. , Rastan Syed Omar S.
Published: March 2005

In Malaysia, pineapples are grown on peat soils, but most K fertilizer recommendations do not take into account K loss through leaching. The objective of this study was to determine applied K use efficiency under a conventionally recommended fertilization regime in pineapple cultivation with residues removal. Results showed that K recovery from applied K fertilizer in pineapple cultivation on tropical peat soil was low, estimated at 28%. At a depth of 0–10 cm, there was a sharp decrease of soil total K, exchangeable K, and soil solution K days after planting (DAP) for plots with K fertilizer. This decline continued until the end of the study. Soil total, exchangeable, and solution K at the end of the study were generally lower than prior values before the study. There was no significant accumulation of K at depths of 10–25 and 25–45 cm. However, K concentrations throughout the study period were generally lower or equal to their initial status in the soil indicating leaching of the applied K and partly explained the low K recovery. Potassium losses through leaching in pineapple cultivation on tropical peat soils need to be considered in fertilizer recommendations for efficient recovery of applied K.
Probing the pH‐dependent structural features of α‐KTx12.1, a potassium channel blocker from the scorpion Tityus serrulatus
Authors: Oyama Sérgio , Pristovšek Primož , Franzoni Lorella , Pertinhez Thelma A. , Schininá Eugenia , Lücke Christian , Rüterjans Heinz , Arantes Eliane Candiani , Spisni Alberto
Published: March 2005

Potassium channels are widespread in living cells and are involved in many diseases. The scorpion toxin α‐KTx12.1 interacts with various K+ channels, suggesting its capacity to match diverse channel pores. It is recognized that tissue injuries may affect the pH at toxins site of action, thereby modulating both protein conformation and activity. To better understand its molecular mechanism of action, we studied α‐KTx12.1 using pH as a tool to explore its plasticity and NMR in combination with MD calculations to detect it. The toxin solution structure consists of an α‐helix and a triple‐stranded β‐sheet stabilized by four disulfide bridges. The NMR results show, in addition, that His28 possesses an unusually low pKa of 5.2. The best set of protein conformers is obtained at pH 4.5, while at pH 7.0, the reduced number of NOEs resulting from a faster hydrogen exchange does not allow to reach a good structural convergence. Nonetheless, MD calculations show that the toxin structure does not vary significantly in that pH range, while conformational changes and modifications of the surface charge distribution occur when His28 is fully protonated. Moreover, essential dynamics analysis reveals variations in the toxin's coherent motions. In conclusion, His28, with its low pKa value, provides α‐KTx12.1 with the ability to preserve its active conformation over a wide pH interval, thus expanding the range of cellular conditions where the toxin can fully exhibit its activity. Overall, the results further underline the role of histidine as a natural controller of proteins' functionality.
Influence of denatured and intermediate states of folding on protein aggregation
Authors: Fawzi Nicolas L. , Chubukov Victor , Clark Louis A. , Brown Scott , Head‐Gordon Teresa
Published: March 2005

We simulate the aggregation thermodynamics and kinetics of proteins L and G, each of which self‐assembles to the same β/β topology through distinct folding mechanisms. We find that the aggregation kinetics of both proteins at an experimentally relevant concentration exhibit both fast and slow aggregation pathways, although a greater proportion of protein G aggregation events are slow relative to those of found for protein L. These kinetic differences are correlated with the amount and distribution of intrachain contacts formed in the denatured state ensemble (DSE), or an intermediate state ensemble (ISE) if it exists, as well as the folding timescales of the two proteins. Protein G aggregates more slowly than protein L due to its rapidly formed folding intermediate, which exhibits native intrachain contacts spread across the protein, suggesting that certain early folding intermediates may be selected for by evolution due to their protective role against unwanted aggregation. Protein L shows only localized native structure in the DSE with timescales of folding that are commensurate with the aggregation timescale, leaving it vulnerable to domain swapping or nonnative interactions with other chains that increase the aggregation rate. Folding experiments that characterize the structural signatures of the DSE, ISE, or the transition state ensemble (TSE) under nonaggregating conditions should be able to predict regions where interchain contacts will be made in the aggregate, and to predict slower aggregation rates for proteins with contacts that are dispersed across the fold. Since proteins L and G can both form amyloid fibrils, this work also provides mechanistic and structural insight into the formation of prefibrillar species.
Evolution of distinct EGF domains with specific functions
Authors: Wouters Merridee A. , Rigoutsos Isidore , Chu Carmen K. , Feng Lina L. , Sparrow Duncan B. , Dunwoodie Sally L.
Published: March 2005

EGF domains are extracellular protein modules cross‐linked by three intradomain disulfides. Past studies suggest the existence of two types of EGF domain with three‐disulfides, human EGF‐like (hEGF) domains and complement C1r‐like (cEGF) domains, but to date no functional information has been related to the two different types, and they are not differentiated in sequence or structure databases. We have developed new sequence patterns based on the different C‐termini to search specifically for the two types of EGF domains in sequence databases. The exhibited sensitivity and specificity of the new pattern‐based method represents a significant advancement over the currently available sequence detection techniques. We re‐annotated EGF sequences in the latest release of Swiss‐Prot looking for functional relationships that might correlate with EGF type. We show that important post‐translational modifications of three‐disulfide EGFs, including unusual forms of glycosylation and post‐translational proteolytic processing, are dependent on EGF subtype. For example, EGF domains that are shed from the cell surface and mediate intercellular signaling are all hEGFs, as are all human EGF receptor family ligands. Additional experimental data suggest that functional specialization has accompanied subtype divergence. Based on our structural analysis of EGF domains with three‐disulfide bonds and comparison to laminin and integrin‐like EGF domains with an additional inter‐domain disulfide, we propose that these hEGF and cEGF domains may have arisen from a four‐disulfide ancestor by selective loss of different cysteine residues.
Multiple sclerosis
Authors: Hafler David A. , Slavik Jacqueline M. , Anderson David E. , O'Connor Kevin C. , De Jager Philip , Baecher‐Allan Clare
Published: March 2005

Summary:  Multiple sclerosis (MS) is a complex genetic disease associated with inflammation in the central nervous system (CNS) white matter and is thought to be mediated by autoimmune processes. Clonal expansion of B cells, their antibody products, and T cells, hallmarks of inflammation in the CNS, are found in MS. The association of the disease with major histocompatibility complex genes, the inflammatory white matter infiltrates, similarities with animal models, and the observation that MS can be treated with immunomodulatory and immunosuppressive therapies support the hypothesis that autoimmunity plays a major role in the disease pathology.

This review discusses the immunopathology of MS with particular focus given to regulatory T cells and the role of B cells and antibodies, immunomodulatory therapeutics, and finally new directions in MS research, particularly new methods to define the molecular pathology of human disease with high‐throughput examination of germline DNA haplotypes, RNA expression, and protein structures that will allow the generation of a new series of hypotheses that can be tested to develop better understandings and therapies for this disease.
The stages of type 1A diabetes: 2005
Authors: Gianani Roberto , Eisenbarth George S.
Published: March 2005

Summary:  Type 1A diabetes is a chronic autoimmune disease usually preceded by a long prodrome during which autoantibodies to islet autoantigens are present. These antibodies are directed to a variety of antigens, but the best characterized are glutamic acid decarboxylase‐65, insulinoma‐associated antigen‐2, and insulin. We hypothesize that the natural history of type 1A diabetes can be represented by several stages, starting from genetic susceptibility and ending in complete β‐cell destruction and overt diabetes. Type 1A diabetes probably results from a balance between genetic susceptibility and environmental influences. In both humans and animal models, the major determinants of the disease are genes within the major histocompatibility complex. The next best‐characterized susceptibility locus is the insulin gene, the variable nucleotide tandem repeat locus. This gene affects the expression of insulin in the thymus and thus may play a role in the modulation of tolerance to this molecule. In a subset of genetically susceptible individuals, the activation of autoimmunity may be triggered by environmental factors such as viruses and/or diet. However, no conclusive association has been established between type 1A diabetes and specific environmental triggers. In this review, we provide evidence that insulin has a fundamental role in anti‐islet autoimmunity.
Regulatory T cells and intestinal homeostasis
Authors: Coombes Janine L. , Robinson Nicholas J. , Maloy Kevin J. , Uhlig Holm H. , Powrie Fiona
Published: March 2005

Summary:  Murine models of inflammatory bowel disease (IBD) are useful tools for the study of the pathogenesis and regulation of intestinal inflammation. Colitis can be induced in immune‐deficient mice following transfer of populations of T cells or following infection with Helicobacter hepaticus and other intestinal pathogens. In these situations, colitis occurs as a result of the absence of a specialized population of regulatory cells, as transfer of CD4+CD25+ T cells prevents disease. Importantly, from a clinical perspective, CD4+CD25+ T cells can also reverse an established colitis. CD4+CD25+ T cells proliferate both in the secondary lymphoid organs and at the site of inflammation, suggesting that regulation occurs both locally and systemically. CD4+CD25+ T cells are not only capable of regulating other T cells but are also capable of suppressing components of the innate immune system. Control of colitis is dependent on the presence of the immunosuppressive cytokines interleukin‐10 and transforming growth factor‐β, although their roles are divergent and complex. Regulatory T cells represent one of the host's mechanisms to prevent immune pathology during chronic immune stimulation. Enhancement of regulatory T‐cell activity may be useful to control autoreactive T‐cell responses and inhibit harmful inflammatory diseases such as asthma and IBD.
A method for double‐stranded RNA‐mediated transient gene silencing in Phytophthora infestans
Authors: WHISSON STEPHEN C. , AVROVA ANNA O. , VAN WEST PIETER , JONES JOHN T.
Published: March 2005

Gene silencing, triggered by double‐stranded RNA (dsRNA), has proved to be a valuable tool for determining and confirming the function of genes in many organisms. For Phytophthora infestans, the cause of late blight on potato and tomato, gene silencing strategies have relied on stable transformation followed by spontaneous silencing of both the endogenous gene and the transgene. Here we describe the first application of transient gene silencing in P. infestans, by delivering in vitro synthesized dsRNA into protoplasts to trigger silencing. A marker gene, gfp, and two P. infestans genes, inf1 and cdc14, both of which have been silenced previously, were selected to test this strategy. Green fluorescent protein (GFP) fluorescence was reduced in regenerating protoplasts up to 4 days after exposure to gfp dsRNA. A secondary reduction in expression of all genes tested was not fully activated until 12–17 days after introduction of the respective homologous dsRNAs. At this time after exposure to dsRNA, reduced GFP fluorescence in gfp dsRNA‐treated lines, and reduced INF1 production in inf1 dsRNA‐treated lines, was observed. Introduction of dsRNA for the stage‐specific gene, cdc14, yielded the expected phenotype of reduced numbers of sporangia when cdc14 expression was significantly reduced compared with control lines. Silencing was shown to be sequence‐specific, because analysis of inf1 expression in gfp‐silenced lines yielded wild‐type levels of gene expression. This report shows that transient gene silencing can be used to generate detectable phenotypes in P. infestans and should provide a high‐throughput tool for P. infestans functional genomics.
Terminal deoxynucleotidyl transferase‐positive cells in trephine biopsies following bone marrow or peripheral stem cell transplantation reflect vigorous B‐cell generation
Authors: Wolf E , Harms H , Winkler J , Reulbach U , Kirchner T , Niedobitek G , Baumann I
Published: March 2005

Aims : Bone marrow is the major site of B‐cell generation in humans. While in early childhood a high number of B‐cell precursors is found in the bone marrow, only very few such cells are usually detectable in adult bone marrow. To assess the number of immature B cells present after haematopoietic cell transplantation the number of terminal deoxynucleotidyl transferase (TdT)‐positive cells in regenerating bone marrow of adult patients was analysed.

Methods and results : Bone marrow biopsy specimens were analysed from patients after allogeneic bone marrow transplantation (BMT; n = 14) or stem cell transplantation (SCT; n = 25) and autologous BMT (n = 9). Specimens from 11 untransplanted adult patients and 11 infants were also studied, as negative and positive controls, respectively. Immunohistochemistry was performed on paraffin‐embedded bone marrow biopsy sections using TdT as a marker of lymphoid progenitors. Immunoreactivity for CD79a, CD20 and CD10 was used to confirm their B‐cell origin. Using computer‐assisted automated image analysis we quantitatively assessed the TdT+ cells present. We found a significant increase in the numbers of B‐cell precursors in the bone marrow after allogeneic and autologous BMT/SCT compared with adult controls (P = 0.022). To analyse this in detail, we followed some patients after allogeneic BMT/SCT for up to 1445 days, when a marked B‐cell increase was still detectable. However, the median number of TdT+ B cells after BMT/SCT was significantly lower than the number of equivalent B cells in infantile bone marrow biopsy specimens (P < 0.001).

Conclusions : Bone marrow of adult patients after BMT/SCT is capable of initiating vigorous precursor B‐cell generation, which is not seen in untransplanted adults. However, the increase of immature B cells was variable in our study. Only in two young adult patients did it reach the magnitude of B‐cell generation seen in infantile bone marrow where immunocompetent B cells are produced normally. A marked increase in number of immature B cells post‐transplant may mimic B‐cell acute lymphoblastic leukaemia (B‐ALL). This is a potential problem in patients transplanted for B‐ALL itself. Since reactive and neoplastic B‐cell precursors share the same immunophenotype in paraffin‐embedded tissue, additional tools, particularly molecular techniques, may have to be employed to establish the correct diagnosis.
Morphometric analysis of primary graft non‐function in liver transplantation
Authors: Vertemati M , Sabatella G , Minola E , Gambacorta M , Goffredi M , Vizzotto L
Published: March 2005

Aims : Primary graft non‐function (PNF) is a life‐threatening condition that is thought to be the consequence of microcirculation injury. The aim of the present study was to assess, with a computerized morphometric model, the morphological changes at reperfusion in liver biopsy specimens from patients who developed PNF after liver transplantation.

Methods and results : Biopsy specimens were obtained at maximum ischaemia and at the end of reperfusion. Morphology included many stereological parameters, such as volumes of all parenchymal components, surface density, size distribution and mean diameter of hepatocytes. Other variables examined were intensive care unit stay, degree of steatosis, serum liver function tests and ischaemic time. In the postoperative period, the PNF group showed elevated serum levels of alanine transferase, decreased daily rate of bile production and prothrombin activity. Blood lactates were significantly higher in the PNF group than in a control group. When comparing groups, the volumetric parameters related to hepatocytes and sinusoids and the surface densities of the hepatic cells showed an inverse relationship. At the end of reperfusion, in PNF group the volume fraction of hepatocyte cytoplasm was decreased; in contrast, the volume fraction of sinusoidal lumen was markedly increased. The cell profiles showed the same inverse trend: the surface density of the parenchymal border of hepatocytes was decreased in PNF when compared with the control group, while the surface density of the vascular border was increased. In the PNF group, the surface density of the sinusoidal bed was directly correlated with alanine transferase, daily rate of bile production, prothrombin activity and cold ischaemic time.

Conclusions : The alterations in hepatic architecture, as demonstrated by morphometric analysis in liver transplant recipients that developed PNF, provide additional information that may represent useful viability markers of the graft to complement conventional histological analysis.
Beating the barriers: recruitment of people with intellectual disability to participate in research
Authors: Lennox N. , Taylor M. , Rey‐Conde T. , Bain C. , Purdie D. M. , Boyle F.
Published: March 2005

Background  The health status of people with intellectual disability (ID) is poor, yet very little research has been done on their health needs. There are several barriers to performing this research. The aim of our research was to examine the significant barriers encountered in recruiting adults with ID to participate in research.

Methods  Our project was a randomized controlled trial aiming to improve health advocacy of people with ID. We approached many organizations to recruit participants and kept records of our results. Recruitment was very low for the first 4 months. Then we adopted two new recruitment strategies – in‐service telephone recruitment and meetings with prospective participants. We then monitored the subsequent recruitment rates. We also questioned participants about the difficulties they encountered when considering recruitment.

Results  Initial recruitment of participants yielded less than one‐third of the expected number. Additional strategies implemented were partially successful. Significant barriers to recruitment included several sectoral issues and the challenges arising from the research process.

Conclusions  While this population is a difficult one to reach for research, attempts to do so should not be abandoned, because the potential health benefits for this underserved group far outweigh the recruitment barriers experienced.
Barrier to gene flow between two ecologically divergentPopulusspecies,P. alba(white poplar) andP. tremula(European aspen): the role of ecology and life history in gene introgression
Authors: LEXER C. , FAY M. F. , JOSEPH J. A. , NICA M.‐S. , HEINZE B.
Published: March 2005

The renewed interest in the use of hybrid zones for studying speciation calls for the identification and study of hybrid zones across a wide range of organisms, especially in long‐lived taxa for which it is often difficult to generate interpopulation variation through controlled crosses. Here, we report on the extent and direction of introgression between two members of the ‘model tree’ genusPopulus:Populus alba(white poplar) andPopulus tremula(European aspen), across a large zone of sympatry located in the Danube valley. We genotyped 93 hybrid morphotypes and samples from four parental reference populations from within and outside the zone of sympatry for a genome‐wide set of 20 nuclear microsatellites and eight plastid DNA restriction site polymorphisms. Our results indicate that introgression occurs preferentially fromP. tremulatoP. albaviaP. tremulapollen. This unidirectional pattern is facilitated by high levels of pollen vs. seed dispersal inP. tremula(pollen/seed flow = 23.9) and by great ecological opportunity in the lowland floodplain forest in proximity toP. albaseed parents, which maintains gene flow in the direction ofP. albadespite smaller effective population sizes (Ne) in this species (P. alba Nec.500–550;P. tremula Nec.550–700). Our results indicate that hybrid zones will be valuable tools for studying the genetic architecture of the barrier to gene flow between these two ecologically divergentPopulusspecies.
Ancient and recent evolutionary history of the bruchid beetle, Acanthoscelides obtectus Say, a cosmopolitan pest of beans
Authors: ALVAREZ NADIR , MCKEY DOYLE , HOSSAERT‐MCKEY MARTINE , BORN CÉLINE , MERCIER LÉNY , BENREY BETTY
Published: March 2005

Acanthoscelides obtectus Say is a bruchid species of Neotropical origin, and is specialized on beans of the Phaseolus vulgaris L. group. Since the domestication and diffusion of beans, A. obtectus has become cosmopolitan through human‐mediated migrations and is now a major pest in bean granaries. Using phylogeographic methods applied to mitochondrial DNA (mtDNA) and nuclear microsatellite molecular markers, we show that the origin of this species is probably further south than Mesoamerica, as commonly thought. Our results also indicate that A. obtectus and its Mesoamerican sister species Acanthoscelides obvelatus, two morphologically close species differing principally in voltinism, speciated in allopatry: A. obtectus (multivoltine) arising in Andean America and A. obvelatus (univoltine) in Mesoamerica. In contrast to Mesoamerica where beans fruit once yearly, wild beans in Andean America fruit year‐round, especially in regions showing little or no seasonality. In such habitats where resources are continuously present, multivoltinism is adaptive. According to existing hypotheses, multivoltinism in A. obtectus is a new adaptation that evolved after bean domestication. Our data suggest the alternative hypothesis that multivoltinism is an older trait, adapted to exploit the year‐round fruiting of wild beans in relatively aseasonal habitats, and allowed A. obtectus to become a pest in bean granaries. This trait also permitted this species to disperse through human‐mediated migrations associated with diffusion of domesticated beans. We also show that diversity of Old World A. obtectus populations can be quite well explained by a single colonization event about 500 bp. Human‐mediated migrations appear not to be rare, as our results indicate a second more recent migration event from Andean America to Mexico.