Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

Autologous peripheral stem-cell transplantation after intensive chemotherapy in a case of CD30 (Ki-1)-positive anaplastic large-cell lymphoma

Simultaneous treatment with peripheral blood stem-cell (PBSC) transplantation and intensive chemotherapy was evaluated in a case of non-Hodgkin's lymphoma (NHL) with poor prognosis. A 59-year-old male diagnosed with a high-grade, anaplastic large-cell (Ki-1) NHL, involving fractures in the left hip, underwent computed tomography and gallium scintigram surveillance. The patient received chemotherapy with epirubicin hydrochloride, cyclophosphamide, vincristine and prednisolone, and the fractured hip bone was repaired following the first course of chemotherapy. After the second and third courses of chemotherapy, PBSCs were harvested and cryopreserved. The patient then received a further course of chemotherapy and PBSC transplantation was conducted using infused cells consisting of 9.63 x 10(6)/kg CD34 cells and 2.24 x 10(5)/kg granulocyte macrophage colony-forming units. Recovery of platelet and white blood cell counts occurred 10 and 8 days, respectively, after PBSC infusion and the patient remains well.

Purpura due to aspirin-induced platelet dysfunction aggravated by drinking alcohol

We report a rare case of prominent purpura induced by aspirin and enhanced by alcohol. A 44-year-old woman presented with a history of generalized purpura. She drank alcohol once or twice a week and regularly took an analgesic preparation, containing aspirin and acetaminophen, for alleviation of headaches. When purpura was evident the patient's liver function was within normal limits and her coagulation time was normal but her bleeding time was prolonged. Red blood cell, white blood cell and platelet counts were normal but a poor response to platelet agonists demonstrated platelet dysfunction. After stopping the analgesic and abstaining from alcohol for 5 days, platelet aggregation, in response to the agonists, returned to normal and purpura disappeared. When the patient took further doses of the analgesic preparation for 3 days for headache relief, but did not drink alcohol, platelet aggregation was again abnormal but purpura was only slight.

A therapeutic strategy for isolated plasmacytoma of bone

Two cases of solitary plasmacytoma of bone (SPB) were diagnosed. The first case was a 41-year-old woman, complaining of fatigue from her lumbar region to her legs. The second case was a 56-year-old man complaining of poor gait and severe lumbago with numbness in the toes of both feet. Magnetic resonance imaging showed the osteolytic lesion in the 12th thoracic bone in the first patient and around the 2nd, 3rd and 4th lumbar bones in the second patient. In both patients serum analysis revealed the monoclonal component of immunoglobulin G (IgG) protein with kappa-light chain, and considering this and other findings SPB was diagnosed. Both patients were first treated with irradiation around the involved bone and then with a course of chemotherapy. In the first patient the tumour region of the bone was surgically removed and replaced with a ceramic spacer. The symptoms of both patients were ameliorated, and the patients remained in good condition for around 3 years without conversion to multiple myeloma. In view of the overall effectiveness of treatments for SPB, our therapeutic strategy deserves careful evaluation.

Treatment of acute myeloblastic leukaemia in a patient with Bombay blood type: a case report

A 62-year-old female was admitted to our hospital with suspected acute leukaemia and after investigation we diagnosed acute myeloblastic leukaemia (AML-M1). The patient's blood type was found to be the very rare Bombay type and surveillance of her relatives showed the same blood type in her male cousin on her mother's side. Alongside chemotherapy the patient received 4000 ml of frozen Bombay-type red cells, 1400 ml of concentrated red cells in manitol adenine phosphate solutions and 360 units of type O concentrated platelets without marked effects. The anti-H antibody was initially at 128 dilution but for unknown reasons increased to 2048 dilution after remission of AML-M1. About 3 months after hospitalization the patient died of Cryptococcus neoformans pneumonia despite strict precautions against infection. Although AML-M1 is a common adult leukaemia and is chemosensitive to anti-leukaemic drugs, neither AML-M1 in a patient with Bombay-type red cells nor its treatment with chemotherapy and transfusion with type Oh frozen red cells have previously been reported.

The CAG regimen (low-dose cytarabine, aclarubicin hydrochloride and granulocyte colony-stimulating factor) for the treatment of elderly acute myelomonocytic leukaemia: a case study

Elderly patients with acute myelomonocytic leukaemia (AMMoL) frequently have a poor quality of life after induction of remission using high-intensity treatment; we seek a more appropriate regimen for such patients. An 86-year-old man was hospitalized with a diagnosis of AMMoL (FAB classification M4), of abnormal karyotype, and complications of diabetes mellitus and complete right bundle branch block. He was treated with CAG therapy (cytarabine 10 mg/m2 subcutaneously every 12 h for 14 consecutive days; aclarubicin hydrochloride 10 mg/m2 per day, bolus intravenously for 4 consecutive days; granulocyte colony-stimulating factor 100 microg/day, subcutaneous injection for 14 consecutive days) every 3 months. White blood cell counts were at their lowest (around 600 - 800/microl) 12 days after the end of therapy, but returned to about 2000 - 2300/microl 30 days after stopping therapy. No symptoms of drug-related toxicity, except slight nausea, were found. Complete remission with a good quality of life was induced and lasted over 2 years suggesting that CAG therapy might prove effective in elderly patients with AMMoL.

Isolated factor VII deficiency diagnosed after a life-threatening brain haemorrhage

A 65-year-old man was admitted to another hospital with a life-threatening brain haemorrhage, and laboratory examinations on admission revealed prolonged prothrombin time with normal activated partial thromboplastin time. To establish the cause of his abnormal coagulation, he was referred to our clinic. Neither the patient nor his family had any previous history of bleeding symptoms. His liver function was within normal limits but coagulation tests showed increased plasma activities of factors II, VIII, IX, X, with reduced activities of factors V and VII. The activity of factor VII was less than 2% but no inhibitor of factor VII was detected in the plasma. We concluded that the patient had a rare congenital isolated factor VII deficiency although he had not shown earlier bleeding problems, presumably because of compensation for the factor VII deficiency by enhanced activities of components of the extrinsic coagulation pathway, factors II, VIII, IX and X.

Congenital dislocation of the knee reduced spontaneously or with minimal treatment

Six cases of congenital dislocation of the knee (CDK) reduced spontaneously or with minimal treatment were investigated. Reduction was achieved from 4 days to 3 months after birth. Clinical results were good, although in four cases, hyperextension < or = 20 degrees persisted. In view of the perinatal complications and associated anomalies, CDK reduced with no or minimal treatment is supposed to be a category of congenital postural deformity. We believe that it is advisable to wait 1 month for spontaneous reduction of CDK in cases not associated with clubfoot, arthrogryposis multiplex congenita, and Larsen's syndrome.

[Exposure to blood during midwifery operations--a questionnaire study]

A self-administered questionnaire was mailed to all midwives working in Nara Prefecture to investigate blood exposure events at delivery and to consider protective measures for the exposure. Out of the 203 midwives 193 responded to the questionnaire. The median number of deliveries in which the midwives had assisted within the past one year was 35 after excluding those who had not assisted in deliveries at all. The incidence of needle-stick injuries was estimated to be 86.2 per 100 persons within the past one year. The occurrence in the subgroup who had worked as midwife for less than 5 years was 2-3 times higher than that in those who worked for more than 5 years. Over 90% of the midwives had experiences of direct blood contact events to the skin while assisting in their 10 most recent deliveries. Blood contact events occurred in the finger-hand-arm area in 85% of the midwives, on the legs in 62%, in the face in 20% and in the eyes in 1%. Around 20% of the midwives had unintentionally sucked amniotic fluid when using a tracheal catheter on a newborn. The most common occasion where direct blood contact events occurred was while bathing an infant for removing blood and amniotic fluid. The midwives wore a disposal gown more often when assisting in labors of parturient women infected with blood-born infectious diseases than without the diseases, and similarly for wearing gloves when measuring blood loss and for usage of a mechanical device for sucking amniotic fluid in the tracheae of an infant. Based on the results obtained in this questionnaire study and our previous study about blood contact events observed in a delivery room, protective measures for midwives against exposure to blood at delivery are required and some ideas are presented.

[Exposure to blood during midwifery procedures--blood contact events to midwives occurred in a delivery room]

Midwives are often exposed to blood during delivery procedures. A study aimed at clarifying actual status of blood contact during midwifery procedures was performed. Observations in a delivery room were conducted to record blood contact events experienced by midwives from the time of episiotomy until 2 hour after expulsion of the placenta. All gloves used by midwives were collected and tested for holes. Blood contact was defined as any contact with blood of a parturition woman as recognized visually by an observer. During a one-month study period data was obtained from a total of 19 midwives (12 midwives and 7 student midwives) who assisted in 8 deliveries. All of the midwives wore gowns with long sleeves, gloves and caps but did not use eye protection or masks. None of the parturient women had Hepatitis B, Hepatitis C or acquired immunodeficiency syndrome. Deliveries caused widespread blood exposure to the midwives throughout the complete course. Protection from most of this exposure was provided by the gowns and gloves. However, direct blood contacts occurred to the fingers, hands or forearms in several midwives. These events were caused by partly because the midwives unintentionally performed procedures without gloves and partly because blood penetrated the gown and soaked to the skin. Direct blood contacts to the foot in two midwives and to the mouth in one also occurred. The overall perforation rate for gloves examined was 4 out of 154 (2.6%). Two gloves were broken during washing sharp instruments contaminated with blood, one was torn when wearing, and the remaining one appeared to have had a hole prior to use.(ABSTRACT TRUNCATED AT 250 WORDS)

Primary small cell carcinoma of the larynx

Small cell carcinoma is a rare tumor of the larynx. We present such a case in a 78-year-old female. The histopathological diagnosis at the time of laryngomicroscopic biopsy was squamous cell carcinoma, upon which basis we initially chose surgical treatment. The surgical specimen, however, revealed small cell carcinoma. Despite the administration of radiotherapy and chemotherapy, the patient died 9 months after initial presentation. We believe that this case illustrates the need for a sufficiently large biopsy specimen in order to arrive at the correct histopathological diagnosis when small cell carcinoma of the larynx is present, and that immunohistochemistry and electron microscopy should be performed to aid the diagnosis.

Recurrent dislocation of the patella in Kabuki make-up syndrome

Three patients with Kabuki make-up syndrome (KMS) who had recurrent dislocation of the patella are reported. In all, dislocation of the patella developed in adolescence, and they had generalized ligamentous laxity and dysplasia of the patellofemoral joints. In two of the three patients, surgical intervention was required; the operation was successful in one, but yielded poor results in the other. In the third patient, cardiac complications precluded operation. Orthopedists should be aware of this possible complication when treating patients with KMS.

Laryngomicrosurgery with carbon dioxide laser for laryngeal papillomatosis: application of a two-stage operation

Among the many treatments reported, CO2 laser surgery has recently been applied in the field of laryngomicrosurgery to treat laryngeal papilloma. It is exceedingly difficult to cure this disease, however, because of its rapid recurrence following surgery. Incomplete removal of papilloma is believed to be caused by the difficulty of precisely identifying residual papillomas during surgery. In an effort to resolve this problem, we have developed a new surgical method which we call the "two-stage operation," in which a series of two operations are performed about 10 days apart. By the time of the second operation, the bleeding, coagulated blood, and carbonized tissue from the first operation have resolved, and the laryngeal image is much clearer. If additional lesions are found, they are removed at the second operation. We applied this method to several patients with recurrent laryngeal papillomatosis and obtained good results. This new method is clearly useful in the treatment of laryngeal papillomatosis, and it promises to decrease the recurrence rate. In this paper we present the case of a 26-year-old male with laryngeal papilloma who underwent surgery 1 month previously at another hospital. Laryngeal endoscopy revealed multiple papillomas especially of the glottis. The first operation with the CO2 laser was performed on April 16, 1990. Visible lesions appeared to have been completely removed. The second operation was carried out 10 days after the first operation, and the small residual lesions were removed with the CO2 laser. The patient has been disease-free for 18 months.

Beneficial effects of a calcium antagonist, nifedipine, on death and cardiovascular calcinosis induced by dietary magnesium deficiency in adult mice

The effects of nifedipine on the survival rate and the cardiovascular calcinosis were investigated in dietary magnesium (Mg)-deficient mice. Male mice aged 8 to 10 weeks were fed with a diet which was either normal (0.07%) or deficient (0.007%) in Mg for 30 d. Nifedipine was added to the Mg-deficient diet for 30 d in a concentration of 1000 ppm. About 65% of Mg-deficient mice died within 30 d. In contrast, all the nifedipine-treated mice survived for 30 d. Mg-deficient mice showed hypomagnesaemia and hypocalcaemia which were not influenced by nifedipine treatment. Aortic and cardiac calcium contents increased in Mg-deficient mice, and these increments were normalized by nifedipine treatment. These results suggest that the life-saving effect of nifedipine in Mg-deficient mice might relate, at least in part, to the prevention of a deleterious increase in Ca in cardiovascular tissues.

An insertion of Escherichia coli transposable element IS1K into the site immediately before tetracycline-resistance determinant of Bacillus subtilis chromosomal DNA fragment in cloning in E. coli

In cloning in Escherichia coli C600 of a 4.5-kbp HindIII DNA fragment with the tetracycline-resistance determinant (tetBS908) from Bacillus subtilis GSY908 chromosome using a plasmid vector, a 5.2-kbp HindIII DNA fragment was also isolated at a ratio of 2 to 89. The two independently obtained 5.2-kbp fragments were an insertion derivative of the 4.5-kbp fragment and carried E. coli transposable element ISlK, which was inserted at the same site immediately before tetBS908 in the same direction. For the ISlK insertions, the 8-bp sequence CAAATTTT was used as a target, this having no similarity to any published sequences.

Promoter sequence analysis in Bacillus and Escherichia: construction of strong promoters in E. coli

Many derivatives of the nprM promoter of Bacillus stearothermophilus and the strong early promoter, A3, of coliphage T3 were designed and chemically synthesized. These promoters consisted of some or all of the AT box, consensus sequence, tac promoter sequence, spacer, and lac operator. The promoter activities were assessed by their ability to express the cat gene in Escherichia coli. One of the derivatives of the A3 promoter, which contained the lac operator, was much stronger (about 3.5 times) than the tac promoter. The promoter activities in E. coli were considerably modified by the substitutions in the -43 (AT box) and -35 regions.

An NMR study on the conformation of a deoxyoligonucleotide duplex, d(GGGGCCCC)2, and its complex with chromomycin

The conformation of drug-free d(GGGGCCCC)2 and the chromomycin-d(GGGGCCCC)2 complex in aqueous solution were studied by NMR spectroscopy. The present study has indicated that free d(GGGGCCCC)2 takes the B form in solution, although it takes the A form in the crystalline state. The NMR spectrum of the complex indicated that chromomycin binds as a symmetry-related dimer to the minor groove of the central four residues of d(GGGGCCCC)2. The drastic conformational change in the central four residues of d(GGGGCCCC)2 on going from the B form family to the A form was demonstrated by the characteristic NOEs and coupling patterns. The change seems to be indispensable for accommodation of the bulky chromomycin dimer in the minor groove. On the basis of the intermolecular NOEs between chromomycin and d(GGGGCCCC)2, the structure of the complex has been constructed and refined by energy minimization.

Deformation of crowns during cementation

Deformation of crowns during cementation was investigated by a simple loading system of defined crowns with silicone fluids as cements. Deformation of the crowns was measured by long stain gauges that encircled the cervical margins. Die spacing was simulated by etching the die. Venting was simulated by removing a small screw. Deformation of the crowns was decreased by decreasing the viscosity of fluid, increasing the thickness of the crowns, and venting. Etching the die decreased the seating times of the crowns, but did not alter the level of deformation. Terminal cementation with zinc phosphate cement confirmed the presence of crown deformation during cementation. The results have consequences for bonded and all-ceramic crowns, and explain several clinical phenomena. It is suggested that low viscosity cements, low seating forces, and die spacing be used to decrease the deformation of crowns during seating. The importance of passive fitting of the crown to the tooth is stressed.

A short-term evaluation of the effectiveness of stabilization-type occlusal splint therapy for specific symptoms of temporomandibular joint dysfunction syndrome

To clarify the short-term effectiveness of stabilization-type occlusal splint therapy, a specific symptom approach was used toward 30 temporomandibular joint dysfunction patients with more than two major symptoms (temporomandibular joint and/or masticatory muscle pain, temporomandibular joint sounds, and limitation of mandibular movement). Eighty-seven percent of the patients with pain responded with this therapy and more than 50% had complete relief of pain 4 weeks after insertion of the splint. Temporomandibular joint sounds and limitation of mandibular movement responded more slowly than pain. These results suggest that the stabilization-type occlusal splint should be selected as a first choice among several therapies and that temporomandibular joint pain is particularly susceptible to this therapy.

Nucleotide sequence homology of the tetracycline-resistance determinant naturally maintained in Bacillus subtilis Marburg 168 chromosome and the tetracycline-resistance gene of B. subtilis plasmid pNS1981

The nucleotide sequence (1579 bp) of tetracycline-resistance determinant and flanking regions of the cloned 5.1 kb DNA fragment from Bacillus subtilis GSY908 chromosome (Sakaguchi, R. and Shishido, K. (1988) Biochim. Biophys. Acta 949, 49-57) were determined and compared with those of the B. subtilis tetracycline-resistance plasmid pNS1981. The tetracycline-resistance structural (tet) genes of the B. subtilis GSY908 chromosome (tetBS908) and pNS1981 (tetpNS1981) were found to be highly homologous (80% identical). Both tet genes were composed of 1374 bp and 458 amino-acid residues initiating from a GTG codon preceded by a ribosome-binding site (RBS-2). Upstream from tetBS908 there exists a short open reading frame (20 amino acids) initiating from a ATG codon preceded by its own RBS (RBS-1). This leader sequence was also highly homologous to that of tetpNS1981 except for a deletion of one bp between the RBS-1 and the ATG codon.

Molecular cloning of a tetracycline-resistance determinant from Bacillus subtilis chromosomal DNA and its expression in Escherichia coli and B. subtilis

Bacillus subtilis GSY908 DNA fragments (5.1 and 4.4 kilobase pairs (kb)) containing a tetracycline-resistance determinant were cloned in Escherichia coli using a shuttle plasmid vector pLS353. Restriction endonucelase analysis showed that the 4.4 kb fragment is a spontaneous deletion derivative of the 5.1 kb fragment. E. coli tetracycline-resistance transformants carrying pLS353 with the 5.1 kb fragment (named pTBS1) and that with 4.4 kb fragment (pTBS1.1) could grow at tetracycline concentrations up to 80 and 50 micrograms per ml, respectively. B. subtilis MI112 and RM125 were transformed by pTBS1, resulting in isolation of transformants of MI112 maintaining pTBS1 and RM125 maintaining either pTBS1 or pTBS1.1. Maximum tetracycline concentrations permitting growth of plasmidless MI112 and MI112 with pTBS1 were 4 and 10 micrograms per ml, respectively, while those of plasmidless RM125, RM125 with pTBS1 and RM125 with pTBS1.1 were 7, 50 and 80 micrograms per ml, respectively. It was interesting to note that the tetracycline-resistance level in E. coli conferred by the 5.1 kb fragment is higher than that conferred by the 4.4 kb fragment, but in B. subtilis the 4.4 kb fragment, in contrast, confers a higher level of tetracycline resistance. The level of tetracycline resistance in B. subtilis conferred by the cloned determinant clearly depends on the host strain. The tetracycline resistance conferred by the cloned determinant was associated with decreased accumulation of the drug into the cells. However, it was constitutive in E. coli, but inducible in B. subtilis. The cloned tetracycline-resistance determinant was detected specifically on the chromosome of B. subtilis Marburg 168 derivatives.

Enhancement of S1 nuclease-susceptibility of negatively superhelical DNA by netropsin

It was evidenced that the antibiotic netropsin enhances the single-strand-specific nuclease S1-susceptibility of negatively superhelical DNA. In contrast, an intercalating drug inhibited S1 action on the superhelical DNA. Negatively superhelical DNA is known to possess several (or a number of) unbasepaired sites sensitive to S1 cleavage. S1 cleaves generally the DNA once at these sites to result in production of the full-length linear form. However netropsin-bound DNA had a tendency to be cleaved by S1 simultaneously at plural sites producing several species of linear DNAs smaller than full-length size.

Soft tissue collagen in congenital dislocation of the hip. Biochemical studies of the ligamentum teres of the femur and the hip joint capsule

Collagens of the ligamentum teres of the femur and the hip joint capsule of 14 patients with congenital dislocation of the hip (CDH) were studied biochemically. Collagen was a major component of these tissues. Solubility of collagen was reversely related to age except in two cases. Collagen of both ligamentum teres of the femur and hip joint capsule was composed of type I, III and V collagens except in three cases. In these three cases with nevus or general joint laxity, two additional collagenous components were also found. The ratios of type III collagen to type I collagen were increased in CDH except in one case with short stature. These abnormalities of collagen metabolism could be the underlying cause of CDH and other clinical symptoms in these patients.

The treatment of congenital dislocation of the knee with the Pavlik harness

We have used the Pavlik harness in the treatment of congenital dislocation of the knee in six knees in five patients, with satisfactory results. We believe that the muscles in the thigh which cross both the hip and knee joints, the rectus femoris and hamstrings, play an important role in the spontaneous reduction of the joint. Full correction is not always obtained, our results are comparable with those described by other authors. We consider that the advantages of using the harness are that a spontaneous correction can be obtained, maximal correction can be obtained after three months of treatment and the method is safer than others used.

Study of an intravenous fat tolerance test with Intralipid. II. The relation between K2 and PHLA with special reference to clinical data in human subjects

The relation between K2 and PHLA was studied in human subjects with special reference to clinical data determined by routine laboratory and physical examinations. The results obtained by Multiple Regression Analysis indicated that those factors which may contribute to K2 variation were fasting triglyceride level and age. There was an inverse partial correlation between K2 and fasting triglyceride level and between K2 and age. The first and second principal components calculated by Principal Component Analysis indicated that K2 is closely related to obesity and hyperlipidemia, especially hypertriglyceridemia, while PHLA related to albumin. These two components also suggested that K2 fibes different clinical information from that obtained by PHLA measurement. There was no partial correlation between K2 and PHLA. The various lipoprotein paper electrophoretic patterns, type IIa, type IIb, type IV and normal patterns, were clearly characterized by such factors as K2, plasma triglyceride and degree of obesity which has high coefficients in the first principal component.