The complex polyploid genome architecture of sugarcane.

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Heritability of arterial stiffness and carotid intima-media thickness: an Italian twin study.

BACKGROUND AND AIMS: Carotid intima-media thickness (IMT) and arterial stiffness parameters, including aortic augmentation index (AIx) and pulse wave velocity (PWV), are independent predictors of stroke and cardiovascular disease. Genetic effects on these traits were never explored in a Mediterranean country. The present study aims to quantify the contribution of genes, environment and age to carotid IMT and aortic Aix and PWV. METHODS AND RESULTS: The twin design was used. A total of 348 adult twins from the Italian Twin Register underwent measurements of carotid IMT and aortic PWV and AIx in three university hospitals located in Rome, Padua and Perugia. Carotid IMT was measured by B-mode ultrasound, aortic PWV and AIx by Arteriograph. Genetic modelling was performed to decompose total variance of traits into genetic, shared and unshared environmental and age components. For each phenotype, the best-fitting model included additive genetic, unshared environmental and age effects. For IMT, heritability was 0.32 (95% confidence interval (CI): 0.25-0.38), unshared environmental component was 0.25 (0.18-0.32) and age contribution was 0.44 (0.39-0.49). For AIx and PWV, heritabilities were 0.42 (0.29-0.55) and 0.49 (0.35-0.62), unshared environmental components were 0.31 (0.22-0.44) and 0.37 (0.26-0.51) and age contributions were 0.27 (0.16-0.39) and 0.14 (0.06-0.24), respectively. CONCLUSION: This study shows substantial genetic and unshared environmental influences on carotid intima-media thickness and arterial stiffness and confirms the relevant role of age in the aetiology of these traits. Further support is provided for prevention and health promotion strategies based on modifiable factors.

Field survey data on the effectiveness of agrometeorological services for smallholder farmers in Niger.

The dataset contains the answers of smallholder farmers to a semi-structured field survey and the 2020 yield plot measurements conducted in 8 municipalities of the Dosso and Tillabéri regions in Niger. It is a systematic sampling of about 320 questionnaires and 192 yield plot samples equally distributed in eight municipalities of intervention. The dataset contains several pieces of information about the uptake and the impacts of a tailored climate service (CS) produced by the National Meteorological Service (NMS) and disseminated through a network that involves Ministry of Agriculture extension services at the municipal level developed in the context of the AdaptatioN Au changement Climatique, prévention des catastrophes et Développement agrIcole pour la sécurité Alimentaire du Niger (ANADIA) Project. The material gathered by the survey gives a picture of the preferences of local farmers in the broadcasting of climate services information and their consequent strategical and tactical decisions in farm practices. Moreover, the survey investigates the preferences regarding the information that farmers would like to receive during the cropping season. Furthermore, the measurement of yield and its relation to the farmers' access to climate information and participation in training initiatives gives an indication of the impact of the CS on agricultural production in these regions. The dataset could benefit further studies and investigations about CSs for smallholder farmers in semi-arid regions. This article is a co-submission of the article: "Effectiveness of agrometeorological services for smallholder farmers: the case study in the regions of Dosso and Tillabéri in Niger" submitted to the journal Climate Services.

A congenital tympanic membrane cholesteatoma (CTMC) in the adult: a case report.

OBJECTIVE: We present an additional very rare case of a congenital tympanic membrane cholesteatoma (CTMC) in the adult. METHOD: Case report and literature review of CTMC. CASE REPORT: A 54-year old man was referred to us by his primary care physician who noted a white mass on the right tympanic membrane without prior history of otorrhea, tympanic perforations or previous otologic procedures. The pearl was about 5 mm diameter, centered on the umbo of a normal tympanic membrane (TM). The audiogram and the tympanogram was absolutely normal. CT confirmed a soft round shape tissue mass, located in the centre of the TM near umbo. The mass protruded both in the auditory canal and in the middle ear space, touching the malleus extremity, without any relationship with medial wall of the cavum tympani. A surgical excision was performed using a "minimal" retroauricolar transcanalar approach: the CTMC was located into the thickness of the TM, between epidermic and mucous layers. The ossicular chain was preserved intact. A partial myringoplasty (underlay technique) using a temporalis fascia graft was necessary. Histopathology confirmed a cystic cholesteatoma. After two months and one year follow-up, otoendoscopy showed a well-healed TM with a preserved normal audiogram and tympanogram. DISCUSSION: This exceptional (probably the first reported) case showed the possible localization of the CC in the TM, also in the adult. Criteria for classification of a TM cholesteatoma as congenital and possible pathogenetic mechanisms are discussed.

Diagnostic accuracy of colour Doppler ultrasonography, CT angiography and blood-pool-enhanced MR angiography in assessing carotid stenosis: a comparative study with DSA in 170 patients.

PURPOSE: This study was undertaken to prospectively evaluate the diagnostic performance of colour Doppler ultrasonography (CDUS), first-pass (FP) and steady-state (SS) contrast-enhanced magnetic resonance angiography (MRA) and computed tomography angiography (CTA) of the carotid arteries using digital subtraction angiography (DSA) as the reference standard. MATERIALS AND METHODS: A total of 170 patients with previous cerebrovascular events and suspected carotid artery stenoses underwent CDUS, blood-pool MRA, CTA and DSA. Accuracy, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated for CDUS, FP MRA, SS MRA and CTA. The McNemar and Wilcoxon tests and receiver operating characteristic (ROC) curve analysis were used to determine significant differences (p<0.05) between the diagnostic performances of the four modalities, and the degree of stenosis was compared using linear regression. RESULTS: A total of 336 carotid bifurcations were studied. The area under the curve (AUC) for degree of stenosis was: CDUS 0.85±0.02, FP MRA 0.982±0.005, SS MRA 0.994±0.002 and CTA 0.997±0.001. AUC analysis showed no statistically significant difference between CTA and MRA (p=0.0174) and a statistically significant difference between CDUS and the other techniques (p<0.001). Plaque morphology analysis showed no significant difference between CTA and SS MRA; a significant difference was seen between CTA and SS MRA versus FP MRA (p=0.04) and CDUS (p=0.038). Plaque ulceration analysis showed a statistically significant difference between MRA and CTA (0.04< p<0.046) versus CDUS (p=0.019). CONCLUSIONS: CTA is the most accurate technique for evaluating carotid stenoses, with a slightly better performance than MRA (97% vs. 95% for SS MRA and 92% for FP MRA) and a greater accuracy than CDUS (97% vs. 76%). Blood-pool contrast-enhanced SS sequences offer improved evaluation of degree of stenosis and plaque morphology with accuracy substantially identical to CTA.

Preliminary experience with MRA in evaluating the degree of carotid stenosis and plaque morphology using high-resolution sequences after gadofosveset trisodium (Vasovist) administration: comparison with CTA and DSA.

PURPOSE: The authors performed a preliminary study with blood-pool contrast-enhanced magnetic resonance angiography (MRA) in evaluating the degree of carotid artery stenosis and plaque morphology, comparing the diagnostic performance of first-pass (FP) and steady-state (SS) acquisitions with 64-slice computed tomography angiography (CTA) and using digital subtraction angiography (DSA) as the reference standard. MATERIALS AND METHODS: Twenty patients with >or=50% carotid artery stenosis at Doppler sonography underwent blood-pool contrast-enhanced MRA, CTA and DSA. Two independent radiologists evaluated MRA and CTA examinations to assess the degree of stenosis and characterise plaque morphology. Accuracy, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated for FP, SS and CTA. The McNemar and Wilcoxon tests were used to determine significant differences (p<0.05) between the diagnostic performance of the three modalities. RESULTS: Forty carotid bifurcations were studied. For stenosis grading, accuracy, sensitivity, specificity, PPV and NPV were 90%, 89%, 90%, 89% and 90%, respectively, at FP; 95%, 95%, 95%, 95% and 95%, respectively, at SS; and 97.5%, 95%, 100%, 100% and 95%, respectively, at CTA. SS and CTA were superior to FP for evaluating the degree of stenosis (p<0.05). For evaluating plaque morphology, accuracy, sensitivity, specificity, PPV and NPV were 87.5%, 89%, 86%, 85% and 90%, respectively, at FP; 97.5%, 100%, 95%, 95% and 100%, respectively, at SS; and 100%, 100%, 100%, 100% and 100%, respectively, at CTA. There were no significant differences between FP, SS and CTA for plaque assessment (p>0.05). CONCLUSIONS: Blood-pool contrast-enhanced MRA with SS sequences allow improved diagnostic evaluation of the degree of carotid stenosis and plaque morphology compared with FP and is substantially equal to CTA and DSA.

Diagnostic performance of 64-MDCT and 1.5-T MRI with high-resolution sequences in the T staging of gastric cancer: a comparative analysis with histopathology.

PURPOSE: This study was undertaken to compare the accuracy of magnetic resonance (MR) imaging and 64-slice multidetector computed tomography (64-MDCT) in the T staging of gastric carcinoma in comparison with histopathology. MATERIALS AND METHODS: Forty patients with an endoscopic diagnosis of gastric carcinoma underwent preoperative MR imaging and 64-MDCT, both of which were performed after i.v. injection of scopolamine and water distension of the stomach. In the MR imaging protocol, we acquired T2-weighted turbo spin-echo (TSE) sequences, true fast imaging steady-state free precession (true-FISP) and gadolinium-enhanced T1-weighted volumetric interpolated breath-hold examination (VIBE) 3D sequences. Contrastenhanced CT scans were obtained in the arterial and venous phases. Two groups of radiologists independently reviewed the MR and 64-MDCT images. The results were compared with pathology findings. RESULTS: In the evaluation of T stage, 64-MDCT had 82.5% and MR imaging had 80% sensitivity. Accuracy of MR imaging was slightly higher than that of 64-MDCT in identifying T1 lesions (50% vs 37.5%), whereas the accuracy of 64-MDCT was higher in differentiating T2 lesions (81.2% vs 68.7%). The accuracy of MR imaging and 64-MDCT did not differ significantly in the evaluation of T3-T4 lesions (p>0.05). Understaging was observed in 20% of cases with MR imaging and in 17.5% with 64-MDCT. CONCLUSIONS: MR imaging and 64-MDCT accuracy levels did not differ in advanced stages of disease, whereas MR imaging was superior in identifying early stages of gastric cancer and can be considered a valid alternative to MDCT in clinical practice.

Imaging the whole body atherosclerosis: high resolution magnetic resonance angiography using blood-pool agent. Initial clinical experience.

AIM: Recently whole-body 3D MR angiography (MRA) with blood-pool contrast agent has become available. The purpose of this study was to introduce and evaluate this technique to demonstrate arterial steno-occlusive involvement in systemic atherosclerosis and to compare blood-pool enhanced MRA results with those of CT angiography (CTA) as reference modality. METHODS: Twenty patients with clinically and US documented carotid occlusive disease underwent whole-body MRA on a 1.5 T scanner and CTA on a 64-MDCT unit. Ten milliliters of a blood-pool agent (MS-235 Gadofosveset Trisodium, VASOVIST, Schering, Berlin, Germany) were administered intravenously and four 3-D MRA stations were acquired successively through automatic table moving. Images were reviewed by two observers. Overall image quality of each arterial segment was assessed and rated for both MRA and CTA examinations; MRA sensitivity, MRA specificity interobserver and intermodality agreement were calculated. RESULTS: Whole-body MRA with blood-pool contrast agent was well tolerated by all patients. It yielded a detailed display of the arterial system with a short examination time. In 14 out of 20 patients there was extensive involvement of the arterial bed by steno-occlusive atherosclerotic disease; for the identification and characterization of vessel damage in the various vascular districts MRA sensitivity was 92-100%, MRA specificity was 95-100%; in 2 cases MRA underestimated the degree of peripheral vessel stenosis. Interobserver agreement calculated with K value was 0.63, intermodality agreement with CTA was 93% (P<0.01). CONCLUSION: The whole-body MRA technique is a valuable tool for comprehensive evaluation of arterial steno-occlusive involvement in systemic arterial atherosclerosis; there is a good agreement between blood-pool enhanced MRA results and CTA, used as modality of reference.

Cochlear effects of mesna application into the middle ear.

Mesna (sodium 2-mercapto-ethane sulphonate) belongs to a class of thiol compounds that produce mucolysis by disrupting the disulphide bonds of the mucus polypeptide chains. The registered indications of mesna include the treatment of pathologies of the respiratory tract and, in oncology, the prevention of toxic lesions of the urinary tract by antineoplastic agents. In the E.N.T. Clinic of the University of Parma, it has been found that mesna can be used to facilitate the dissection of the various tissue layers in any surgical procedure. One of these indications is surgical treatment of cholesteatoma, which is mainly composed by keratin, a protein rich is disulphide bonds that are easily disrupted by mesna. The aim of this study was to evaluate the toxicity of mesna application into the middle ear on the cochlear anatomy and physiology. Three groups of guinea pigs were used as subjects. Mesna solution (10 or 20%) was applied in one ear, while the opposite ear received a placebo (saline solution). Toxicity of mesna was assessed by means of transmission electron microscopy (TEM), scanning electron microscopy (SEM), and auditory brain-stem response (ABR). TEM and SEM did not show any toxic effect on cochlear morphology. There were no differences in ABR thresholds and wave III amplitude and latency between mesna-treated and control ears.

Chemically assisted dissection of tissues: an interesting support in abdominal myomectomy.

BACKGROUND: The aim of this study was to verify the efficacy of sodium-2-mercaptoethanesulfonate (mesna) in the chemical separation of tissues in abdominal myomectomies when used with the traditional mechanical separation techniques. STUDY DESIGN: In a prospective, randomized study, 58 women underwent abdominal myomectomy. In 29 of these, we used mesna for highlighting and separating tissues, and in the other 29 we used saline solution for the same purposes. The variables evaluated included the number of myomas removed, the volume of the biggest myoma, and the total volume of the myomas removed in every intervention. We also recorded operating time, the length of hospital stay, the degree of procedure difficulty, perioperative blood loss, operative complications, and cost. RESULTS: The operation was significantly shorter in the mesna group (p < 0.05) even though the volume and the number of myomas were larger. The degree of difficulty evaluated by the surgeon at the end of every operation was not significantly different in the two groups. The reduction in hemoglobin 24 hours after operation was significantly less in the patients treated with mesna (p = 0.006), but this difference was probably altered by the increase in hematocrit levels. CONCLUSIONS: Because of its ability as a chemical dissector, mesna may be a useful aid in this type of benign gynecologic operation. Larger studies to confirm this are needed.

Facial-nerve and vocal-cord monitoring during otoneurosurgical operations.

We describe a newly developed instrument to monitor facial muscles and vocal-cord function during neurosurgical and otoneurosurgical operations. The device (Myo-Alarm) transforms into acoustic signals the pressure variations that are induced by facial muscles and vocal-cord contractions on air-inflated rubber sensors that are positioned, respectively, beneath the superior lip and between the vocal cords. It represents an effective and dependable method to monitor facial and vocal-cord functional preservation during surgery.

Regenerated middle ear mucosa after tympanoplasty. Part II. Scanning electron microscopy.

The ultrastructural appearance of the regenerated middle ear epithelium, found at the second operation of staged ICWT with mastoidectomy, has been investigated herein with the scanning electron microscope. The regenerated epithelium consists of flat nonciliated cells, "elevated" nonciliated cells with microvilli, and ciliated cells. Secretory material is present on the surface of the "elevated" nonciliated cells surrounding the ciliated ones. Regeneration of the mucosa occurs following precise topographic differences that mimic the distribution of epithelial cells in the normal middle ear. It is confirmed that a morphologically normal middle ear epithelium regenerates to cover all denuded bone surfaces within 12 months--after first stage ICWT with mastoidectomy--when silicone rubber sheeting has been used to maintain an aerated middle ear and mastoid space.

Regenerated middle ear mucosa after tympanoplasty. Part I. Transmission electron microscopy.

The ultrastructural appearance of the regenerated middle ear mucosa--found at the second operation of staged intact canal wall tympanoplasty (ICWT) with mastoidectomy--has been evaluated with the transmission electron microscope. The regenerated epithelium showed all the morphologic characteristics of the normal middle ear mucosa: ciliated cells, nonciliated cells, and secretory cells. All of these (including goblet cells) have been found in the specimens. It is concluded that a normal middle ear mucosa regenerates to cover all denuded bone surfaces after the first operation of staged ICWT with mastoidectomy, when silicone rubber sheeting has been used to prevent adhesions and maintain an air-containing middle ear space.

Failures with Plasti-Pore ossicular replacement prostheses.

Plasti-Pore ossicular prosthesis failures found in our series of 246 patients with regular follow-up are reported and analyzed. Extrusions as well as poor functional results (postoperative air-bone gap greater than 25 dB) of the prostheses with and without cartilage on top have been reviewed. The overall extrusion rate was 9.3%: a higher extrusion rate occurred with prostheses without cartilage (18.4%) than with cartilage (4.4%). Thirty-six patients among those with poor postoperative hearing improvement have undergone revision surgery: the main causes of failure were a short prosthesis, a fixed stapes or footplate, adhesions of the prosthesis to surrounding structures, and the displacement of the prosthesis.

Histology of extruded Plasti-Pore ossicular prostheses.

Twenty-three Plasti-Pore ossicular prostheses removed from the human middle ear following partial or total extrusion were investigated by light microscopy. No specific tissue reaction other than the ingrowth of histiocytic cells elicited from the porous Plasti-Pore was found. The only histologic feature typical of extruded prostheses was the presence of granulocytes in all parts extruded. In our opinion this finding was the inflammatory reaction following the ischemic necrosis of tissue grown inside the pores and the superimposed bacterial colonization. We concluded that no histologic feature supports a biologic cause of extrusion, and that extrusion instead is related to biofunctional characteristics.

Subjective tinnitus, temporomandibular joint dysfunction, and serotonin modulation of neural plasticity: causal or casual triad?

Tinnitus and temporomandibular joint dysfunction (TMJD) are among the most common complaints encountered by physicians. Though the relationship between tinnitus and TMJD has attracted great interest during the past several years, theories attempting to explain this association are still few and inconsistent. Conceivably, TMJD could irritate auricolo-temporal nerve (ATN), triggering a somatosensory pathway-induced disinhibition of dorsal cochlear nucleus (DCN) activity in the auditory pathway. In genetically-predisposed TMJD patients, signals from cronically stimulated DCNs activating specific cortical neuronal networks, could yield plastic neural changes resulting in tinnitus. Based on current evidence of serotoninergic modulation of neural activity and plasticity in sensory pathways, reduced serotoninergic tone could promote plastic changes underlying tinnitus through diminished filtering of incoming signals. Therefore, the early establishment of specific treatments aimed at improving TMJD and/or boosting serotoninergic activity may be required to prevent the creation of 'tinnitus memory circuits'.

Molded tympanic heterografts. Histologic evaluation.

The histologic appearance of the molded tympanic heterograft developed at the ENT Clinic of the University of Parma, Italy, is investigated with light and electron microscopy. Evaluation of the graft before insertion disclosed a unique structure of interwoven collagen bundles. Examination of grafted tympanic membrane showed a structure closely resembling the normal human tympanic membrane. The fate of the heterologous material and the host reaction to it are discussed in relation to histologic findings.

Prevention of recurrent cholesteatoma in closed tympanoplasty.

Recurrent cholesteatoma in a series of 534 staged intact canal wall tympanoplasties performed over a 10-year period has been reviewed for the present study. Overall detected incidence of recurrent cholesteatoma is 5.2% (28 of 534 operated ears). A steady decrease of recurrent cholesteatoma was found, however, in the second period of our surgical experience (1978 to 1982) when prevention techniques were adopted in all operations, resulting in a 1.07% incidence (four of 373 operated ears). Our present policy for prevention of recurrent cholesteatoma in intact canal wall tympanoplasties with mastoidectomy includes the use of plastic sheeting with thick Silastic, the repair of bony sulcus defects with cartilage shavings, staging of the operation with preplanned reexploration of the middle ear and mastoid, and transtympanic ventilation tube insertion in cases of refractory tubal insufficiency.

Paradoxical effects of contralateral white noise on evoked otoacoustic emissions in ears with acoustic neuroma.

A contralateral suppression effect on evoked otoacoustic emissions (EOAEs) is usually present in normally hearing subjects and in patients with sensorineural hearing loss, while it is absent or reduced in ears to which the vestibular nerve has been cut and in ears with acoustic neuroma (AN). To date, a paradoxical effect, that is an increase in EOAE amplitude during contralateral stimulation, has been described in one ear with sensorineural hearing loss of unknown aetiology and in three ears with AN (two in the present paper). Evidence has been provided that the contralateral suppression effect on EOAEs is accomplished largely, if not entirely, via the medial olivocochlear bundle (OCB). According to clinical data the absence or the reduced amount of contralateral suppression effect on EAOEs may be attributed to a totally, or partially, damaged or malfunctioning medial OCB. The way in which a contralateral noise may increase EOAE amplitude is more difficult to explain. One attractive hypothesis is that this paradoxical effect is a result of some pathological adaptive process in the medial OCB.

Scutumplasty: costal cartilage versus bone paté.

This study was carried out to evaluate the anatomical and hearing results of the reparation of attic defects in closed tympanoplasty. Reparation was carried out in 194 patients by using a costal cartilage allograft, and in 159 patients with a bone pate autograft. The follow-up was from 1 to 5 years. The study was not truly randomized owing to an occasional lack of allogenic costal cartilage. In the group 'costal cartilage' a partial resorption was observed in 5.7% and a complete resorption in 4.7% of the cases. In the group 'bone pate', partial resorption was observed in 5.5% and total resorption in 2.7% of the patients. Satisfactory hearing results were obtained in 86% of the patients of the group 'costal cartilage' and in 82% of the patients of the group 'bone paté'. Both graft materials may be recommended for repairing erosions caused by the cholesteatoma in the wall of the external auditory canal.